BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231803.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,885,687 number of mapped reads = 2,402,188 (83.24%) number of supplementary alignments = 19,966 (0.69%) number of secondary alignments = 0 number of mapped bases = 155,109,367 bp number of sequenced bases = 155,048,123 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 109,789 duplication rate = 2.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0209 >>>>>>> ACTG content number of A's = 45,448,253 bp (29.31%) number of C's = 30,905,852 bp (19.93%) number of T's = 44,612,808 bp (28.77%) number of G's = 34,070,022 bp (21.97%) number of N's = 11,188 bp (0.01%) GC percentage = 41.91% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 889,113 number of insertions = 10,938 mapped reads with insertion percentage = 0.45% number of deletions = 36,569 mapped reads with deletion percentage = 1.51% homopolymer indels = 45.27% >>>>>>> Coverage mean coverageData = 0.0501X std coverageData = 3.3262X There is a 4.3% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 15548366 0.06238045039815568 0.853461975276719 chr2 243199373 11943715 0.04911079684403627 11.783860868598966 chr3 198022430 16215284 0.08188609744865771 0.32114148322204555 chr4 191154276 5717230 0.02990898304571539 0.20984057500288522 chr5 180915260 6287259 0.03475250788684161 0.2112456211136471 chr6 171115067 11458839 0.06696569274054634 0.3335434537764902 chr7 159138663 10894665 0.06846020190580589 0.5723380954189099 chr8 146364022 7830518 0.05350029257873223 0.565148340114725 chr9 141213431 8165613 0.057824620095803775 0.3348697721108601 chr10 135534747 6432119 0.04745734317119432 0.3344842782123527 chr11 135006516 5569883 0.04125640128362397 0.2924865367356221 chr12 133851895 5054599 0.037762625624388806 0.22064152327419867 chr13 115169878 4263721 0.03702114714404751 0.214236322552218 chr14 107349540 6559905 0.06110790041578194 0.29593355987921055 chr15 102531392 2918825 0.02846762287202733 0.1888669021295775 chr16 90354753 3970144 0.043939514725915965 0.25739246945901634 chr17 81195210 4095256 0.05043716248778715 0.26569182602483254 chr18 78077248 2810145 0.03599185514325505 0.5477025729054478 chr19 59128983 4522126 0.07647900861071803 0.5278560530283041 chr20 63025520 3776573 0.05992133028017857 0.2784946886511691 chr21 48129895 3208734 0.0666682110983205 0.29850823110018687 chr22 51304566 1608376 0.031349568379547346 0.19530315025210765 chrMT 16571 161971 9.774364854263473 6.385956672100334 chrX 155270560 5787830 0.037275772045904904 0.23288744881724954 chrY 59373566 307671 0.005181952520756459 0.11171759882757482