BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10251053.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP224945/SRP224945.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 = 1,402,546 number of mapped reads = 1,338,475 (95.43%) number of supplementary alignments = 37,869 (2.7%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 671,694 number of mapped paired reads (second in pair) = 666,781 number of mapped paired reads (both in pair) = 1,330,922 number of mapped paired reads (singletons) = 7,553 number of mapped bases = 165,175,989 bp number of sequenced bases = 165,032,452 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 253,821 duplication rate = 17.3% >>>>>>> Insert size mean insert size = 79,566.52 std insert size = 2,637,865.8887 median insert size = 192 >>>>>>> Mapping quality mean mapping quality = 53.3013 >>>>>>> ACTG content number of A's = 49,145,307 bp (29.78%) number of C's = 33,054,005 bp (20.03%) number of T's = 49,114,415 bp (29.76%) number of G's = 33,713,391 bp (20.43%) number of N's = 5,334 bp (0%) GC percentage = 40.46% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,256,359 number of insertions = 26,951 mapped reads with insertion percentage = 1.9% number of deletions = 70,480 mapped reads with deletion percentage = 5.07% homopolymer indels = 44.82% >>>>>>> Coverage mean coverageData = 0.0534X std coverageData = 0.7073X There is a 3.2% of reference with a coverageData >= 1X There is a 1.31% of reference with a coverageData >= 2X There is a 0.33% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 13315889 0.0534236943786792 1.585308054661041 chr2 243199373 14454951 0.05943662938637593 0.8268794322035413 chr3 198022430 10830815 0.05469488986676913 0.34650000041117285 chr4 191154276 10969228 0.057384162308773044 0.45619659694591413 chr5 180915260 9742736 0.05385248320125124 0.34750812436563283 chr6 171115067 9393758 0.05489731655249271 0.40461694186995395 chr7 159138663 8885116 0.055832541461027604 0.9840604379031257 chr8 146364022 8310926 0.056782574613862415 0.512316589736464 chr9 141213431 7149357 0.05062802418560314 0.9632163710008376 chr10 135534747 9627822 0.07103582079951792 0.7584330117006229 chr11 135006516 7379718 0.05466193942816804 0.4655487263633469 chr12 133851895 7217739 0.05392332323722425 0.3496343224169491 chr13 115169878 5284845 0.045887389061921205 0.3165339291410349 chr14 107349540 4971644 0.04631267167050739 0.33496718026256456 chr15 102531392 4410187 0.04301304131323995 0.3050975285903955 chr16 90354753 4560522 0.050473515211756484 0.48261223284268734 chr17 81195210 4059011 0.04999076915990488 0.43678746917461775 chr18 78077248 4293802 0.05499427951149098 0.6913461200667217 chr19 59128983 3064202 0.05182233558794678 0.7701418079293669 chr20 63025520 3264408 0.05179501890662703 0.34660870664627463 chr21 48129895 2242247 0.046587406849734454 0.35100441656590237 chr22 51304566 1733683 0.0337919825693487 0.2737394334430186 chrMT 16571 213402 12.878039949309034 7.591258289915805 chrX 155270560 9375590 0.06038227723272203 0.38493991813053935 chrY 59373566 424391 0.007147810525647053 0.3964318439074305