BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524433.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 = 1,145,979
number of mapped reads = 1,055,819 (92.13%)
number of supplementary alignments = 3,948 (0.34%)
number of secondary alignments = 0
number of mapped bases = 61,599,476 bp
number of sequenced bases = 61,578,786 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 37,050
duplication rate = 2.68%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.6683
>>>>>>> ACTG content
number of A's = 15,445,078 bp (25.08%)
number of C's = 11,814,286 bp (19.19%)
number of T's = 19,508,126 bp (31.68%)
number of G's = 14,810,053 bp (24.05%)
number of N's = 1,243 bp (0%)
GC percentage = 43.24%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 308,563
number of insertions = 5,110
mapped reads with insertion percentage = 0.48%
number of deletions = 12,894
mapped reads with deletion percentage = 1.21%
homopolymer indels = 42.01%
>>>>>>> Coverage
mean coverageData = 0.0199X
std coverageData = 0.2066X
There is a 1.82% of reference with a coverageData >= 1X
There is a 0.12% 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 4914542 0.01971727083480366 0.3211254416715446
chr2 243199373 5270414 0.02167116606834344 0.27805138303630367
chr3 198022430 4130196 0.020857212993497756 0.15478027284696683
chr4 191154276 3945030 0.020637937495052425 0.16476241805660952
chr5 180915260 3775901 0.02087110285776888 0.1543933602042196
chr6 171115067 3550116 0.020746951523561628 0.1694284502133772
chr7 159138663 3480383 0.02187012844263999 0.295032123577908
chr8 146364022 3113843 0.02127464767263638 0.22969761124327132
chr9 141213431 2606208 0.01845580821557972 0.17587039673478824
chr10 135534747 2960969 0.021846567507887847 0.20559061774602308
chr11 135006516 2806963 0.020791314991048283 0.17852544272164692
chr12 133851895 2737071 0.020448503922936616 0.15427899230414868
chr13 115169878 1884225 0.01636039763800045 0.13773533889884879
chr14 107349540 1846987 0.017205355514331968 0.14528566534768741
chr15 102531392 1724962 0.016823745063365567 0.13900261388816654
chr16 90354753 1718861 0.019023470740936008 0.1559853257045562
chr17 81195210 1660367 0.020449075752128728 0.158083062620886
chr18 78077248 1665142 0.021326853118593524 0.28869981688963414
chr19 59128983 1247323 0.021094951015815714 0.24721834253149028
chr20 63025520 1308581 0.02076271643613571 0.1559216379543437
chr21 48129895 814616 0.016925364162959426 0.15248337529664216
chr22 51304566 727962 0.014189029491059334 0.12757290919161224
chrMT 16571 5387 0.32508599360328283 0.6250345112653479
chrX 155270560 3507025 0.02258654184025613 0.1697969898140391
chrY 59373566 196402 0.0033079030489763742 0.10031121582164997