BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524801.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 = 1,069,256
number of mapped reads = 959,328 (89.72%)
number of supplementary alignments = 3,509 (0.33%)
number of secondary alignments = 0
number of mapped bases = 54,449,326 bp
number of sequenced bases = 54,432,266 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 31,742
duplication rate = 2.55%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.3836
>>>>>>> ACTG content
number of A's = 13,429,325 bp (24.67%)
number of C's = 9,977,645 bp (18.33%)
number of T's = 17,761,849 bp (32.63%)
number of G's = 13,256,979 bp (24.36%)
number of N's = 6,468 bp (0.01%)
GC percentage = 42.69%
>>>>>>> Mismatches and indels
general error rate = 0.0053
number of mismatches = 281,970
number of insertions = 3,772
mapped reads with insertion percentage = 0.39%
number of deletions = 10,627
mapped reads with deletion percentage = 1.1%
homopolymer indels = 41.55%
>>>>>>> Coverage
mean coverageData = 0.0176X
std coverageData = 0.1807X
There is a 1.61% of reference with a coverageData >= 1X
There is a 0.11% 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 4343402 0.017425842240930665 0.22550800839637386
chr2 243199373 4571325 0.018796615071865336 0.2933617957956192
chr3 198022430 3605514 0.018207604057782746 0.14680514130031058
chr4 191154276 3444406 0.018018984832962878 0.16130491469864586
chr5 180915260 3283965 0.0181519513610958 0.1448300463175182
chr6 171115067 3104310 0.018141652014781375 0.15656351977423957
chr7 159138663 3014367 0.01894176401368912 0.20307641616138536
chr8 146364022 2722827 0.01860311682334064 0.16898485160887255
chr9 141213431 2325274 0.016466379887051963 0.15598224381100528
chr10 135534747 2655652 0.019593883183328626 0.21130455452443153
chr11 135006516 2472674 0.01831521968910004 0.16322830599566546
chr12 133851895 2458186 0.018364969730163327 0.1467038119849454
chr13 115169878 1658906 0.014403991988252344 0.12948750526566238
chr14 107349540 1610914 0.015006249677455534 0.13364548111625216
chr15 102531392 1560327 0.015218041709606361 0.1336071830551476
chr16 90354753 1617856 0.017905599277107203 0.15345039652181655
chr17 81195210 1584831 0.01951877456810568 0.15494801449862608
chr18 78077248 1401301 0.01794762284654295 0.21502728753625514
chr19 59128983 1224435 0.020707865041412938 0.19940701176295617
chr20 63025520 1160672 0.01841590517618895 0.15153869006038903
chr21 48129895 706050 0.014669676715480057 0.1419036828346282
chr22 51304566 696155 0.013569065178331301 0.12640733652077135
chrMT 16571 5844 0.3526642930420614 0.6659485040310952
chrX 155270560 3027314 0.01949702506386272 0.15996502941092133
chrY 59373566 192819 0.0032475563283498924 0.10168172769292445