BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068164.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 = 1,869,338 number of mapped reads = 1,612,694 (86.27%) number of supplementary alignments = 13,715 (0.73%) number of secondary alignments = 0 number of mapped bases = 109,182,963 bp number of sequenced bases = 109,136,645 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 129,579 duplication rate = 6.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5784 >>>>>>> ACTG content number of A's = 31,402,193 bp (28.77%) number of C's = 20,636,093 bp (18.91%) number of T's = 33,986,027 bp (31.14%) number of G's = 22,975,153 bp (21.05%) number of N's = 137,179 bp (0.13%) GC percentage = 39.96% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 911,022 number of insertions = 7,734 mapped reads with insertion percentage = 0.48% number of deletions = 26,067 mapped reads with deletion percentage = 1.6% homopolymer indels = 48.18% >>>>>>> Coverage mean coverageData = 0.0353X std coverageData = 0.3539X There is a 2% of reference with a coverageData >= 1X There is a 0.81% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% 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 7601486 0.030497360325533553 0.4417439455574694 chr2 243199373 10763046 0.044256059821338435 0.3891451570635619 chr3 198022430 7085759 0.03578260806111712 0.30370559078268694 chr4 191154276 6131963 0.03207860754315535 0.2918550804798862 chr5 180915260 5087613 0.028121524961465385 0.2705892704114411 chr6 171115067 6735059 0.03935982446244783 0.34920624510982967 chr7 159138663 7665791 0.048170512781045546 0.441100137267419 chr8 146364022 5035805 0.034406030465601714 0.3828694172350207 chr9 141213431 4332559 0.030680927227099242 0.3364976416316237 chr10 135534747 3991216 0.02944791714555678 0.38205774083340727 chr11 135006516 6659363 0.04932623400192032 0.41868997486922366 chr12 133851895 6958809 0.051988871730205985 0.3781005519989256 chr13 115169878 2560188 0.022229666684200185 0.24276895489637662 chr14 107349540 3994855 0.03721352695130319 0.32341711974059223 chr15 102531392 2347350 0.022893964026158935 0.24256567722410988 chr16 90354753 4396435 0.04865748457084488 0.3650728722095032 chr17 81195210 3433817 0.042290881444853705 0.3565001629561089 chr18 78077248 3347380 0.04287266887275535 0.5441827742003104 chr19 59128983 1454463 0.02459813996800858 0.3340077683617082 chr20 63025520 1811888 0.02874848156746664 0.279536900650428 chr21 48129895 1542348 0.0320455301221829 0.292178566697725 chr22 51304566 1260170 0.02456253114001588 0.2517803874323532 chrMT 16571 9622 0.5806529479210669 1.0844338136574636 chrX 155270560 4747428 0.030575197255680666 0.2921485380492319 chrY 59373566 228550 0.0038493561259231087 0.1086326183394511