BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472718.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 26,734,234 number of mapped reads = 26,501,758 (99.13%) number of supplementary alignments = 88,211 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,291,744 number of mapped paired reads (second in pair) = 13,210,014 number of mapped paired reads (both in pair) = 26,362,620 number of mapped paired reads (singletons) = 139,138 number of mapped bases = 2,608,240,294 bp number of sequenced bases = 2,607,861,989 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,350,984 duplication rate = 48.8% >>>>>>> Insert size mean insert size = 22,658.3924 std insert size = 1,477,723.5803 median insert size = 240 >>>>>>> Mapping quality mean mapping quality = 55.2192 >>>>>>> ACTG content number of A's = 715,097,237 bp (27.42%) number of C's = 592,446,920 bp (22.72%) number of T's = 710,102,359 bp (27.23%) number of G's = 589,707,488 bp (22.61%) number of N's = 507,985 bp (0.02%) GC percentage = 45.33% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 15,735,547 number of insertions = 147,898 mapped reads with insertion percentage = 0.55% number of deletions = 144,430 mapped reads with deletion percentage = 0.54% homopolymer indels = 44.86% >>>>>>> Coverage mean coverageData = 0.8425X std coverageData = 24.5876X There is a 7.58% of reference with a coverageData >= 1X There is a 3.31% of reference with a coverageData >= 2X There is a 1.4% of reference with a coverageData >= 3X There is a 0.95% of reference with a coverageData >= 4X There is a 0.67% of reference with a coverageData >= 5X There is a 0.58% of reference with a coverageData >= 6X There is a 0.52% of reference with a coverageData >= 7X There is a 0.49% of reference with a coverageData >= 8X There is a 0.47% of reference with a coverageData >= 9X There is a 0.45% of reference with a coverageData >= 10X There is a 0.43% of reference with a coverageData >= 11X There is a 0.42% of reference with a coverageData >= 12X There is a 0.41% of reference with a coverageData >= 13X There is a 0.4% of reference with a coverageData >= 14X There is a 0.39% of reference with a coverageData >= 15X There is a 0.38% of reference with a coverageData >= 16X There is a 0.37% of reference with a coverageData >= 17X There is a 0.37% of reference with a coverageData >= 18X There is a 0.36% of reference with a coverageData >= 19X There is a 0.35% of reference with a coverageData >= 20X There is a 0.35% of reference with a coverageData >= 21X There is a 0.34% of reference with a coverageData >= 22X There is a 0.34% of reference with a coverageData >= 23X There is a 0.33% of reference with a coverageData >= 24X There is a 0.32% of reference with a coverageData >= 25X There is a 0.32% of reference with a coverageData >= 26X There is a 0.31% of reference with a coverageData >= 27X There is a 0.31% of reference with a coverageData >= 28X There is a 0.31% of reference with a coverageData >= 29X There is a 0.3% of reference with a coverageData >= 30X There is a 0.3% of reference with a coverageData >= 31X There is a 0.29% of reference with a coverageData >= 32X There is a 0.29% of reference with a coverageData >= 33X There is a 0.29% of reference with a coverageData >= 34X There is a 0.28% of reference with a coverageData >= 35X There is a 0.28% of reference with a coverageData >= 36X There is a 0.28% of reference with a coverageData >= 37X There is a 0.27% of reference with a coverageData >= 38X There is a 0.27% of reference with a coverageData >= 39X There is a 0.27% of reference with a coverageData >= 40X There is a 0.26% of reference with a coverageData >= 41X There is a 0.26% of reference with a coverageData >= 42X There is a 0.26% of reference with a coverageData >= 43X There is a 0.26% of reference with a coverageData >= 44X There is a 0.25% of reference with a coverageData >= 45X There is a 0.25% of reference with a coverageData >= 46X There is a 0.25% of reference with a coverageData >= 47X There is a 0.24% of reference with a coverageData >= 48X There is a 0.24% of reference with a coverageData >= 49X There is a 0.24% of reference with a coverageData >= 50X There is a 0.24% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 253972684 1.0189450400607025 30.68454553314607 chr2 243199373 190362164 0.7827411791888131 22.841049377148916 chr3 198022430 306344637 1.5470198855755886 32.39602258329759 chr4 191154276 121509568 0.6356623066072558 23.258174091233528 chr5 180915260 140411818 0.7761192615813614 22.706413762295544 chr6 171115067 167752363 0.9803482880908436 22.392132015143307 chr7 159138663 131204343 0.8244655354431374 25.927853995923 chr8 146364022 104441176 0.7135713720684719 17.42191229811148 chr9 141213431 139536984 0.9881282751355287 21.85329148766453 chr10 135534747 76342653 0.5632699709101165 20.637441074635714 chr11 135006516 123692218 0.9161944302006875 30.94106274479773 chr12 133851895 121072461 0.9045255653646144 22.675672172524376 chr13 115169878 52512396 0.4559559922430412 15.127314939119696 chr14 107349540 73018787 0.6801965523093998 21.37689819305247 chr15 102531392 67030520 0.653756071116249 18.154289956990375 chr16 90354753 79286563 0.8775029577027342 21.364201865780093 chr17 81195210 93939784 1.1569621409932926 23.175519147967467 chr18 78077248 43748361 0.5603215036472597 16.940677809392476 chr19 59128983 57616682 0.9744236933687833 22.886381082618296 chr20 63025520 59474711 0.9436607742387528 37.08016918318712 chr21 48129895 11931348 0.24789889942622978 9.463711145890718 chr22 51304566 23388296 0.4558716274882824 10.80577573513496 chrMT 16571 3582 0.21616076277834773 0.5689293944138684 chrX 155270560 164737687 1.0609718094660057 35.87628888563952 chrY 59373566 4908508 0.08267160507084921 2.932191310381076