BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524984.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 = 724,959
number of mapped reads = 668,944 (92.27%)
number of supplementary alignments = 1,511 (0.21%)
number of secondary alignments = 0
number of mapped bases = 38,895,635 bp
number of sequenced bases = 38,883,237 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 14,829
duplication rate = 1.68%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.7003
>>>>>>> ACTG content
number of A's = 10,008,273 bp (25.74%)
number of C's = 7,487,829 bp (19.26%)
number of T's = 12,184,396 bp (31.34%)
number of G's = 9,202,287 bp (23.67%)
number of N's = 452 bp (0%)
GC percentage = 42.92%
>>>>>>> Mismatches and indels
general error rate = 0.005
number of mismatches = 187,233
number of insertions = 2,817
mapped reads with insertion percentage = 0.42%
number of deletions = 7,255
mapped reads with deletion percentage = 1.07%
homopolymer indels = 44.25%
>>>>>>> Coverage
mean coverageData = 0.0126X
std coverageData = 0.1405X
There is a 1.18% of reference with a coverageData >= 1X
There is a 0.05% 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 3090640 0.012399728384227376 0.2147743836526371
chr2 243199373 3289792 0.013527140137816062 0.14895753849829818
chr3 198022430 2578939 0.01302346910902972 0.11923964057980489
chr4 191154276 2542369 0.013300089609295478 0.12729124973726036
chr5 180915260 2367868 0.013088271271312325 0.11913953017928103
chr6 171115067 2272535 0.013280741666074326 0.13321727486387064
chr7 159138663 2142243 0.013461486728715322 0.16661770724351768
chr8 146364022 2000727 0.013669527337804369 0.15352023929760236
chr9 141213431 1600818 0.011336159660337125 0.12543429314682153
chr10 135534747 1868844 0.013788670738434329 0.1457550941983211
chr11 135006516 1776577 0.0131591944791761 0.13528208653939733
chr12 133851895 1766905 0.013200448152041478 0.12006985787936923
chr13 115169878 1246777 0.01082554763147357 0.10877063942461104
chr14 107349540 1169997 0.010898947494325547 0.11060231348140065
chr15 102531392 1113606 0.010861122416049905 0.11136903755571985
chr16 90354753 1128126 0.012485519162450701 0.1210315170395453
chr17 81195210 1032986 0.01272225295063588 0.12284266435725119
chr18 78077248 1043756 0.013368247815291851 0.17893938955974503
chr19 59128983 777568 0.013150369929413465 0.15674154867317894
chr20 63025520 825243 0.013093791213464006 0.12074978766670011
chr21 48129895 508625 0.010567756277049846 0.11172932583926644
chr22 51304566 455090 0.008870360583500502 0.09804538905791697
chrMT 16571 1826 0.11019250497857704 0.31447570058890806
chrX 155270560 2175102 0.014008463677853676 0.1292033009004698
chrY 59373566 118676 0.0019988019584338255 0.071171411617323