Why are reads from a region of a gene but not recongined as a mapped reads>

Question

[BenBoErBa]

In IGV, I found three mapped reads of gene AT5G09840 (Chr5 3056998 - Chr5 3063970).

34069e1f-79d8-46b9-be66-677f41f48ad0    16      5   3060089 60 
5664b78b-c754-4157-b127-1998121e33e7    2064    5   3061249 60
5664b78b-c754-4157-b127-1998121e33e7    0       5   3061254 60

But there are more reads found when search through this gene's region. (see the posion column, fourth column)

Why were the rest reads not recoginzed as mapped in IGV? Also, FeatureCount only takes the three reads into quantification.

samtools view -h barcode01_sorted.bam "5:3056998-3063970" It is even more strange to me that, position like 2991166 showed up.

@PG ID:samtools.2   PN:samtools PP:samtools.1   VN:1.15.1   CL:samtools view -h barcode01_sorted.bam 5:3056998-3063970
b77d497c-5739-4a5d-8ac3-30f22765ef89    0   5   2991166     60    
f24102f3-c c2a-4249-a280-8737fe86f981   0   5   2993490     60    
b8cc9740-43a4-438d-bf25-ae2ee8e57ac5    0   5   3055861     60    
b640305e-9531-4400-a989-e747632e0a20    0   5   3055998     60    
11fda952-ad27-46e3-8aea-19f0e656ce97    0   5   3057648     55    
9b3ab731-009e-44da-a586-f506165dbad3    16  5   3057657     60    
8396a971-9af2-4eb2-a048-0d44633542f2    0   5   3057670     60    
5fc88d7c-1348-4f48-bd10-cfe1592151c6    0   5   3057670     60    
8a6738f6-168f-45f2-8981-75b9a07e8fe0    0   5   3057670     60    
cfcbee8a-2cb4-451c-a428-4a5c49e8a04c    0   5   3057670     60    
f8811464-3fb4-4983-a3cb-f6af6eac1aa9    16  5   3057670     60    
36785972-d61f-407b-9bca-dcccf46678bc    16  5   3057679     60    
7aaeac79-c91f-4cf3-b25e-f027f025623d    0   5   3057700     60    
7aaeac79-c91f-4cf3-b25e-f027f025623d    2064    5   3057703 60  17
8396a971-9af2-4eb2-a048-0d44633542f2    2064    5   3057731 5   11
e458d287-0a2a-4dba-be45-47d1d46abce3    16  5   3057733 60  157S17
cfcbee8a-2cb4-451c-a428-4a5c49e8a04c    2064    5   3057735 60  12
ce6c43d0-cd1b-4002-8063-36bef3cbf218    16  5   3057741 60  67S38M
c09f3831-6c2a-4fcf-80b3-2739b2ce8361    16  5   3057748 60  113S23
34069e1f-79d8-46b9-be66-677f41f48ad0    16  5   3060089 60  147S6M
5664b78b-c754-4157-b127-1998121e33e7    2064    5   3061249 60  11
5664b78b-c754-4157-b127-1998121e33e7    0   5   3061254 60  1145S7
594fe825-431a-4597-bc36-2b85afb70aa2    0   5   3063213 38  150S14
1e534ea0-04db-464d-8803-6a2285c0e377    0   5   3063252 60  116S41
1e534ea0-04db-464d-8803-6a2285c0e377    2064    5   3063252 13  78
c926df93-c144-4681-8e59-8480e6ebf9b5    0   5   3063260     60    
08be5701-f204-45c4-8d93-07f117d069b2    0   5   3063264     60    
c926df93-c144-4681-8e59-8480e6ebf9b5    2064    5   3063290 60  77
ab85b47b-12c7-475f-bc9e-7109ff6af7c4    0   5   3063449     60

[Pierre Lindenbaum]

why a screenshot of samtools when you can just copy and paste the text. Save the planet.

[Pierre Lindenbaum]

can you please show us the full ouput of samtools view your.bam '5:3056998-3063970'

[BenBoErBa]

please, check the result.

[Pierre Lindenbaum]

this is not the full output

[Pierre Lindenbaum]

also check your IGV parameters: Min MAPQ, discarded reads, etc...