BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524310.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 = 1,651,198
number of mapped reads = 1,501,363 (90.93%)
number of supplementary alignments = 6,318 (0.38%)
number of secondary alignments = 0
number of mapped bases = 86,369,566 bp
number of sequenced bases = 86,347,339 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 43,841
duplication rate = 1.98%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 43.2544
>>>>>>> ACTG content
number of A's = 21,661,685 bp (25.09%)
number of C's = 15,438,750 bp (17.88%)
number of T's = 27,092,824 bp (31.38%)
number of G's = 22,142,175 bp (25.64%)
number of N's = 11,905 bp (0.01%)
GC percentage = 43.52%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 442,342
number of insertions = 5,441
mapped reads with insertion percentage = 0.36%
number of deletions = 14,040
mapped reads with deletion percentage = 0.93%
homopolymer indels = 40.97%
>>>>>>> Coverage
mean coverageData = 0.0279X
std coverageData = 0.2717X
There is a 2.54% of reference with a coverageData >= 1X
There is a 0.17% of reference with a coverageData >= 2X
There is a 0.02% of reference with a coverageData >= 3X
There is a 0.01% 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 7324518 0.029386157477216478 0.509816081619545
chr2 243199373 5573565 0.022917678328060492 0.3394350493825797
chr3 198022430 6069968 0.030652931589618407 0.19092270973546896
chr4 191154276 4605567 0.024093455277976624 0.17962538861289476
chr5 180915260 5126359 0.02833569152762459 0.18213981015381991
chr6 171115067 5520426 0.0322614840223275 0.2072595121072239
chr7 159138663 3995368 0.02510620564909484 0.35703244331494716
chr8 146364022 8989986 0.06142210276238515 0.3333903733733354
chr9 141213431 3606042 0.025536112071379385 0.21312222451799567
chr10 135534747 4351790 0.03210829766037782 0.26693122780508927
chr11 135006516 4119117 0.03051050513739648 0.22843979616406457
chr12 133851895 3414744 0.02551136089631006 0.17395465992673254
chr13 115169878 2229027 0.01935425337517506 0.14889990157429675
chr14 107349540 1828738 0.017035359443552344 0.151336959241695
chr15 102531392 2631727 0.02566752434220341 0.17373613544519642
chr16 90354753 2658372 0.029421495956056677 0.19534407933325532
chr17 81195210 2513538 0.030956727619769687 0.20728894360757455
chr18 78077248 2042645 0.026161846790501632 0.3700664965963882
chr19 59128983 1520889 0.025721548432517435 0.35791932879435995
chr20 63025520 1915412 0.030391054290389036 0.19046014711443476
chr21 48129895 1241462 0.025793989369808513 0.18197691951171413
chr22 51304566 593316 0.011564584719418541 0.11746426941208019
chrMT 16571 16899 1.0197936153521212 1.1150309840804127
chrX 155270560 4242401 0.02732263604897155 0.2014682464211453
chrY 59373566 237690 0.00400329668593596 0.10999189726789149