BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231717.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 = 712,776 number of mapped reads = 288,197 (40.43%) number of supplementary alignments = 2,904 (0.41%) number of secondary alignments = 0 number of mapped bases = 17,890,131 bp number of sequenced bases = 17,872,736 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,671 duplication rate = 5.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.168 >>>>>>> ACTG content number of A's = 5,000,270 bp (27.98%) number of C's = 2,893,524 bp (16.19%) number of T's = 6,132,692 bp (34.31%) number of G's = 3,845,396 bp (21.52%) number of N's = 854 bp (0%) GC percentage = 37.71% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 185,140 number of insertions = 1,773 mapped reads with insertion percentage = 0.61% number of deletions = 9,909 mapped reads with deletion percentage = 3.36% homopolymer indels = 42.11% >>>>>>> Coverage mean coverageData = 0.0058X std coverageData = 0.122X There is a 0.47% of reference with a coverageData >= 1X There is a 0.08% 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 1304533 0.005233820460571691 0.10982929933353341 chr2 243199373 1419878 0.005838329196679302 0.1102675331601759 chr3 198022430 1171532 0.005916158083707992 0.09245059542552564 chr4 191154276 1294431 0.006771655999994476 0.10265470393661641 chr5 180915260 1027099 0.005677238061620672 0.09227827014207288 chr6 171115067 1090775 0.006374511719648861 0.10822205950287936 chr7 159138663 1237861 0.00777850571736926 0.12666560221028117 chr8 146364022 858960 0.005868655344822377 0.2566327831178575 chr9 141213431 797793 0.00564955468010688 0.10206598069471697 chr10 135534747 810595 0.0059807172547420625 0.09911796850269457 chr11 135006516 859320 0.006365026114739529 0.10034315318341025 chr12 133851895 814396 0.006084306837792621 0.10723660450429352 chr13 115169878 594819 0.005164709821087072 0.08999791949439204 chr14 107349540 669047 0.006232416086738704 0.09784081696537232 chr15 102531392 518337 0.00505539805799184 0.10378112886489607 chr16 90354753 485770 0.005376252868512628 0.09058366188099426 chr17 81195210 328265 0.004042910905704905 0.07698785275585354 chr18 78077248 486882 0.006235901142417314 0.30841641963471006 chr19 59128983 323721 0.005474827801452293 0.09448213962990511 chr20 63025520 344562 0.005467023516823027 0.08895755508908958 chr21 48129895 312978 0.006502777535666762 0.09998699438850564 chr22 51304566 164140 0.0031993253777841137 0.06611807327306177 chrMT 16571 6193 0.3737251825478245 0.691291059619175 chrX 155270560 903504 0.0058189008914503815 0.09480787008234913 chrY 59373566 64740 0.0010903842292376376 0.04332637477839277