BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716457.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt
>>>>>>> Reference
number of bases = 3,095,693,983 bp
number of contigs = 25
>>>>>>> Globals
number of windows = 424
number of reads = 1,008,422
number of mapped reads = 886,016 (87.86%)
number of supplementary alignments = 2,516 (0.25%)
number of secondary alignments = 0
number of mapped bases = 50,857,711 bp
number of sequenced bases = 50,841,364 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 27,710
duplication rate = 2.46%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.9603
>>>>>>> ACTG content
number of A's = 12,890,900 bp (25.36%)
number of C's = 9,368,868 bp (18.43%)
number of T's = 16,580,858 bp (32.61%)
number of G's = 12,000,162 bp (23.6%)
number of N's = 576 bp (0%)
GC percentage = 42.03%
>>>>>>> Mismatches and indels
general error rate = 0.0051
number of mismatches = 252,478
number of insertions = 4,213
mapped reads with insertion percentage = 0.47%
number of deletions = 10,366
mapped reads with deletion percentage = 1.16%
homopolymer indels = 42.66%
>>>>>>> Coverage
mean coverageData = 0.0164X
std coverageData = 0.1698X
There is a 1.5% of reference with a coverageData >= 1X
There is a 0.1% of reference with a coverageData >= 2X
There is a 0.01% of reference with a coverageData >= 3X
There is a 0% of reference with a coverageData >= 4X
There is a 0% of reference with a coverageData >= 5X
There is a 0% of reference with a coverageData >= 6X
There is a 0% of reference with a coverageData >= 7X
There is a 0% of reference with a coverageData >= 8X
There is a 0% of reference with a coverageData >= 9X
There is a 0% of reference with a coverageData >= 10X
There is a 0% of reference with a coverageData >= 11X
There is a 0% of reference with a coverageData >= 12X
There is a 0% of reference with a coverageData >= 13X
There is a 0% of reference with a coverageData >= 14X
There is a 0% of reference with a coverageData >= 15X
There is a 0% of reference with a coverageData >= 16X
There is a 0% of reference with a coverageData >= 17X
There is a 0% of reference with a coverageData >= 18X
There is a 0% of reference with a coverageData >= 19X
There is a 0% of reference with a coverageData >= 20X
There is a 0% of reference with a coverageData >= 21X
There is a 0% of reference with a coverageData >= 22X
There is a 0% of reference with a coverageData >= 23X
There is a 0% of reference with a coverageData >= 24X
There is a 0% of reference with a coverageData >= 25X
There is a 0% of reference with a coverageData >= 26X
There is a 0% of reference with a coverageData >= 27X
There is a 0% of reference with a coverageData >= 28X
There is a 0% of reference with a coverageData >= 29X
There is a 0% of reference with a coverageData >= 30X
There is a 0% of reference with a coverageData >= 31X
There is a 0% of reference with a coverageData >= 32X
There is a 0% of reference with a coverageData >= 33X
There is a 0% of reference with a coverageData >= 34X
There is a 0% of reference with a coverageData >= 35X
There is a 0% of reference with a coverageData >= 36X
There is a 0% of reference with a coverageData >= 37X
There is a 0% of reference with a coverageData >= 38X
There is a 0% of reference with a coverageData >= 39X
There is a 0% of reference with a coverageData >= 40X
There is a 0% of reference with a coverageData >= 41X
There is a 0% of reference with a coverageData >= 42X
There is a 0% of reference with a coverageData >= 43X
There is a 0% of reference with a coverageData >= 44X
There is a 0% of reference with a coverageData >= 45X
There is a 0% of reference with a coverageData >= 46X
There is a 0% of reference with a coverageData >= 47X
There is a 0% of reference with a coverageData >= 48X
There is a 0% of reference with a coverageData >= 49X
There is a 0% of reference with a coverageData >= 50X
There is a 0% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 4181682 0.016777017378022903 0.21416778770126396
chr2 243199373 4152813 0.01707575537211603 0.23074987581070608
chr3 198022430 3340405 0.016868821375437115 0.14050754518176264
chr4 191154276 3277084 0.01714366044314907 0.14855465514863528
chr5 180915260 2957467 0.016347250088245734 0.13704613196069323
chr6 171115067 2985735 0.017448697255864676 0.159444758330115
chr7 159138663 2892432 0.0181755454361207 0.22609513243585366
chr8 146364022 2323322 0.01587358674797827 0.16742207872602138
chr9 141213431 2256386 0.015978550935427663 0.15219257777033673
chr10 135534747 2476192 0.018269794682244843 0.19268963045452497
chr11 135006516 2289921 0.016961559099858557 0.16465227923756828
chr12 133851895 2299191 0.017177127002946053 0.14058815912203712
chr13 115169878 1679543 0.014583179466422635 0.1291043080825185
chr14 107349540 1478244 0.013770380385421306 0.127766368786499
chr15 102531392 1464387 0.014282328284395086 0.129434266023634
chr16 90354753 1585136 0.01754347112210024 0.15467589078450983
chr17 81195210 1417169 0.017453849802223555 0.1483005149520104
chr18 78077248 1397296 0.017896327493510018 0.22048057278291897
chr19 59128983 1059819 0.017923849628869823 0.18888759914008812
chr20 63025520 1050704 0.01667108815603584 0.13972076417713386
chr21 48129895 635577 0.013205451622115527 0.1289912186755589
chr22 51304566 573260 0.01117366434792568 0.11337255835879018
chrMT 16571 2368 0.1429002474201919 0.40645419127086463
chrX 155270560 2931185 0.018877918647295405 0.15790812703183235
chrY 59373566 150393 0.002532995912692864 0.07656739246960349