BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038441.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 81,756,652 number of mapped reads = 81,395,387 (99.56%) number of supplementary alignments = 137,914 (0.17%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 40,799,622 number of mapped paired reads (second in pair) = 40,595,765 number of mapped paired reads (both in pair) = 81,153,570 number of mapped paired reads (singletons) = 241,817 number of mapped bases = 12,088,413,507 bp number of sequenced bases = 12,086,468,265 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,502,066 duplication rate = 38.54% >>>>>>> Insert size mean insert size = 21,607.7626 std insert size = 1,549,011.1486 median insert size = 230 >>>>>>> Mapping quality mean mapping quality = 55.8733 >>>>>>> ACTG content number of A's = 3,019,250,815 bp (24.98%) number of C's = 3,024,189,056 bp (25.02%) number of T's = 3,037,610,480 bp (25.13%) number of G's = 3,004,173,051 bp (24.86%) number of N's = 1,244,863 bp (0.01%) GC percentage = 49.88% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 62,652,754 number of insertions = 591,450 mapped reads with insertion percentage = 0.7% number of deletions = 704,279 mapped reads with deletion percentage = 0.84% homopolymer indels = 46.12% >>>>>>> Coverage mean coverageData = 3.9049X std coverageData = 25.7834X There is a 21.89% of reference with a coverageData >= 1X There is a 14.12% of reference with a coverageData >= 2X There is a 9.24% of reference with a coverageData >= 3X There is a 7.25% of reference with a coverageData >= 4X There is a 5.82% of reference with a coverageData >= 5X There is a 5.06% of reference with a coverageData >= 6X There is a 4.52% of reference with a coverageData >= 7X There is a 4.19% of reference with a coverageData >= 8X There is a 3.94% of reference with a coverageData >= 9X There is a 3.77% of reference with a coverageData >= 10X There is a 3.64% of reference with a coverageData >= 11X There is a 3.53% of reference with a coverageData >= 12X There is a 3.44% of reference with a coverageData >= 13X There is a 3.36% of reference with a coverageData >= 14X There is a 3.29% of reference with a coverageData >= 15X There is a 3.23% of reference with a coverageData >= 16X There is a 3.17% of reference with a coverageData >= 17X There is a 3.12% of reference with a coverageData >= 18X There is a 3.07% of reference with a coverageData >= 19X There is a 3.02% of reference with a coverageData >= 20X There is a 2.98% of reference with a coverageData >= 21X There is a 2.93% of reference with a coverageData >= 22X There is a 2.89% of reference with a coverageData >= 23X There is a 2.85% of reference with a coverageData >= 24X There is a 2.82% of reference with a coverageData >= 25X There is a 2.78% of reference with a coverageData >= 26X There is a 2.74% of reference with a coverageData >= 27X There is a 2.71% of reference with a coverageData >= 28X There is a 2.68% of reference with a coverageData >= 29X There is a 2.64% of reference with a coverageData >= 30X There is a 2.61% of reference with a coverageData >= 31X There is a 2.58% of reference with a coverageData >= 32X There is a 2.55% of reference with a coverageData >= 33X There is a 2.52% of reference with a coverageData >= 34X There is a 2.49% of reference with a coverageData >= 35X There is a 2.47% of reference with a coverageData >= 36X There is a 2.44% of reference with a coverageData >= 37X There is a 2.41% of reference with a coverageData >= 38X There is a 2.38% of reference with a coverageData >= 39X There is a 2.36% of reference with a coverageData >= 40X There is a 2.33% of reference with a coverageData >= 41X There is a 2.31% of reference with a coverageData >= 42X There is a 2.28% of reference with a coverageData >= 43X There is a 2.26% of reference with a coverageData >= 44X There is a 2.23% of reference with a coverageData >= 45X There is a 2.21% of reference with a coverageData >= 46X There is a 2.19% of reference with a coverageData >= 47X There is a 2.16% of reference with a coverageData >= 48X There is a 2.14% of reference with a coverageData >= 49X There is a 2.12% of reference with a coverageData >= 50X There is a 2.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1015333456 4.073544338330856 24.589364296092857 chr2 243199373 1010246401 4.153984397813394 27.851861365364453 chr3 198022430 688819709 3.4784933656252983 22.8654729512929 chr4 191154276 413494802 2.1631470174384173 16.673783552325972 chr5 180915260 518405415 2.865459856730715 21.501486043195484 chr6 171115067 739846197 4.323676517626586 28.891117063096377 chr7 159138663 791829417 4.975719929229266 34.31442627243059 chr8 146364022 371619320 2.539007297845368 18.099767449118954 chr9 141213431 466586026 3.3041193227576207 22.06662833670845 chr10 135534747 372132973 2.745664718730762 17.406004749643152 chr11 135006516 832068855 6.163175524061372 35.70958506007521 chr12 133851895 554347559 4.14149952079498 23.275476931487248 chr13 115169878 389177366 3.3791593145561896 28.603603564370065 chr14 107349540 283257732 2.638648772970988 17.06030646093174 chr15 102531392 311474097 3.037841298399616 18.20404916645122 chr16 90354753 594005496 6.574147748486458 34.7749592269998 chr17 81195210 688154920 8.475314245754152 36.88515944769565 chr18 78077248 116735967 1.4951342419241005 11.4252199728324 chr19 59128983 716045954 12.109898017356395 43.457210014132 chr20 63025520 519746164 8.246598584192562 46.62569744228708 chr21 48129895 93550915 1.9437174130548176 20.22993153487426 chr22 51304566 197490574 3.8493761744325057 20.56932570964071 chrMT 16571 1178248 71.10301128477461 29.205452380870742 chrX 155270560 379604541 2.4447940485305133 18.398532604032816 chrY 59373566 23261403 0.39178046001144684 5.481506729598166