BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237596.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 = 1,224,823 number of mapped reads = 978,079 (79.85%) number of supplementary alignments = 6,113 (0.5%) number of secondary alignments = 0 number of mapped bases = 60,843,127 bp number of sequenced bases = 60,807,586 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 69,380 duplication rate = 6.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2373 >>>>>>> ACTG content number of A's = 16,534,971 bp (27.19%) number of C's = 10,515,762 bp (17.29%) number of T's = 19,904,238 bp (32.73%) number of G's = 13,745,550 bp (22.6%) number of N's = 107,065 bp (0.18%) GC percentage = 39.9% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 611,068 number of insertions = 5,243 mapped reads with insertion percentage = 0.53% number of deletions = 22,507 mapped reads with deletion percentage = 2.27% homopolymer indels = 49.69% >>>>>>> Coverage mean coverageData = 0.0197X std coverageData = 0.2067X There is a 1.57% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.06% 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 5518004 0.022138376136683728 0.2692433240921679 chr2 243199373 5471577 0.02249831869426736 0.23288281277633507 chr3 198022430 4454665 0.022495759697525174 0.1855822004476071 chr4 191154276 3657345 0.019132948927598144 0.17697713165433646 chr5 180915260 3549637 0.019620439978363352 0.17108485746444924 chr6 171115067 3691702 0.02157438304366266 0.19033453755228918 chr7 159138663 3504998 0.022024804870957097 0.2483543790324028 chr8 146364022 3165791 0.021629570961093157 0.32055982764819196 chr9 141213431 2553641 0.018083556088938878 0.18775634008957354 chr10 135534747 2811913 0.020746805245447503 0.21007927901522455 chr11 135006516 2483590 0.018396075045740756 0.19098631825872472 chr12 133851895 3161647 0.023620487405127885 0.1910803989714013 chr13 115169878 2120882 0.018415249167842308 0.16877259990038504 chr14 107349540 1604334 0.014944954584807723 0.1592700946970627 chr15 102531392 1505440 0.014682722731395278 0.148344837698272 chr16 90354753 1395255 0.015441965736987848 0.15716247544497985 chr17 81195210 1408600 0.01734831402000192 0.1677701343165526 chr18 78077248 1450933 0.018583300989297162 0.26658288262204644 chr19 59128983 933931 0.01579480912093482 0.19726990986595638 chr20 63025520 1141687 0.01811467799075676 0.168037436452195 chr21 48129895 809292 0.016814746842892553 0.16342280186809716 chr22 51304566 567150 0.011054571634033509 0.12667410290442574 chrMT 16571 53517 3.229557660973991 3.0617589445643443 chrX 155270560 3643830 0.023467616784534042 0.19340208768411613 chrY 59373566 183766 0.003095081066884209 0.08624996889554919