BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472793.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 = 9,484,308 number of mapped reads = 9,399,322 (99.1%) number of supplementary alignments = 31,665 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,714,546 number of mapped paired reads (second in pair) = 4,684,776 number of mapped paired reads (both in pair) = 9,348,252 number of mapped paired reads (singletons) = 51,070 number of mapped bases = 923,883,397 bp number of sequenced bases = 923,745,350 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,150,249 duplication rate = 43.48% >>>>>>> Insert size mean insert size = 26,707.1802 std insert size = 1,593,629.0566 median insert size = 237 >>>>>>> Mapping quality mean mapping quality = 55.1658 >>>>>>> ACTG content number of A's = 254,633,649 bp (27.57%) number of C's = 208,772,027 bp (22.6%) number of T's = 252,607,733 bp (27.35%) number of G's = 207,555,843 bp (22.47%) number of N's = 176,098 bp (0.02%) GC percentage = 45.07% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 5,527,822 number of insertions = 55,340 mapped reads with insertion percentage = 0.58% number of deletions = 55,812 mapped reads with deletion percentage = 0.59% homopolymer indels = 45.68% >>>>>>> Coverage mean coverageData = 0.2984X std coverageData = 10.1989X There is a 2.92% of reference with a coverageData >= 1X There is a 1.28% of reference with a coverageData >= 2X There is a 0.62% of reference with a coverageData >= 3X There is a 0.49% of reference with a coverageData >= 4X There is a 0.4% of reference with a coverageData >= 5X There is a 0.36% of reference with a coverageData >= 6X There is a 0.33% of reference with a coverageData >= 7X There is a 0.32% of reference with a coverageData >= 8X There is a 0.3% of reference with a coverageData >= 9X There is a 0.29% of reference with a coverageData >= 10X There is a 0.27% of reference with a coverageData >= 11X There is a 0.26% of reference with a coverageData >= 12X There is a 0.25% of reference with a coverageData >= 13X There is a 0.24% of reference with a coverageData >= 14X There is a 0.24% of reference with a coverageData >= 15X There is a 0.23% of reference with a coverageData >= 16X There is a 0.22% of reference with a coverageData >= 17X There is a 0.22% of reference with a coverageData >= 18X There is a 0.21% of reference with a coverageData >= 19X There is a 0.2% of reference with a coverageData >= 20X There is a 0.2% of reference with a coverageData >= 21X There is a 0.19% of reference with a coverageData >= 22X There is a 0.19% of reference with a coverageData >= 23X There is a 0.19% of reference with a coverageData >= 24X There is a 0.18% of reference with a coverageData >= 25X There is a 0.18% of reference with a coverageData >= 26X There is a 0.17% of reference with a coverageData >= 27X There is a 0.17% of reference with a coverageData >= 28X There is a 0.17% of reference with a coverageData >= 29X There is a 0.16% of reference with a coverageData >= 30X There is a 0.16% of reference with a coverageData >= 31X There is a 0.16% of reference with a coverageData >= 32X There is a 0.15% of reference with a coverageData >= 33X There is a 0.15% of reference with a coverageData >= 34X There is a 0.15% of reference with a coverageData >= 35X There is a 0.14% of reference with a coverageData >= 36X There is a 0.14% of reference with a coverageData >= 37X There is a 0.14% of reference with a coverageData >= 38X There is a 0.14% of reference with a coverageData >= 39X There is a 0.14% of reference with a coverageData >= 40X There is a 0.13% of reference with a coverageData >= 41X There is a 0.13% of reference with a coverageData >= 42X There is a 0.13% of reference with a coverageData >= 43X There is a 0.13% of reference with a coverageData >= 44X There is a 0.12% of reference with a coverageData >= 45X There is a 0.12% of reference with a coverageData >= 46X There is a 0.12% of reference with a coverageData >= 47X There is a 0.12% of reference with a coverageData >= 48X There is a 0.12% of reference with a coverageData >= 49X There is a 0.12% of reference with a coverageData >= 50X There is a 0.11% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 100187354 0.4019542803867277 12.076129618385611 chr2 243199373 76869581 0.3160763946541918 11.948953276237239 chr3 198022430 96677282 0.4882137947706227 13.755700903840879 chr4 191154276 35777164 0.18716381735556886 8.444281176380564 chr5 180915260 36081955 0.19944119141746253 5.679572646523311 chr6 171115067 55657356 0.3252627426432297 7.7269331660824685 chr7 159138663 34687110 0.21796783601229577 6.374791981266635 chr8 146364022 54637695 0.37330003817468205 13.934371235097673 chr9 141213431 55277787 0.39144850888864813 10.1264023905996 chr10 135534747 49618179 0.3660919439352331 15.245656267911729 chr11 135006516 35654839 0.2640971714283776 8.620918259019563 chr12 133851895 67317837 0.5029277844740263 16.417207720848744 chr13 115169878 14970142 0.1299831367364998 5.101402561019898 chr14 107349540 26234929 0.24438790329236623 8.397737326609676 chr15 102531392 19345281 0.18867666402110292 6.035050566492587 chr16 90354753 27623315 0.3057206630845419 10.585850465923757 chr17 81195210 27284991 0.3360418798103977 7.434163084599492 chr18 78077248 11292204 0.1446286119100919 4.640671704169472 chr19 59128983 17991406 0.3042738955953293 7.496641078316672 chr20 63025520 22417104 0.3556829677882864 13.201802414553008 chr21 48129895 4570238 0.0949563260007112 3.884807605627674 chr22 51304566 9921934 0.19339280640245549 5.189106949257825 chrMT 16571 954 0.05757045440830366 0.26355907692816793 chrX 155270560 40510155 0.2609004243946824 7.633516170518097 chrY 59373566 3276605 0.055186259151084174 3.4434806046509787