BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472493.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 = 16,774,750 number of mapped reads = 16,517,788 (98.47%) number of supplementary alignments = 65,279 (0.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,298,882 number of mapped paired reads (second in pair) = 8,218,906 number of mapped paired reads (both in pair) = 16,378,188 number of mapped paired reads (singletons) = 139,600 number of mapped bases = 1,625,356,243 bp number of sequenced bases = 1,625,128,497 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,202,186 duplication rate = 46.48% >>>>>>> Insert size mean insert size = 31,715.933 std insert size = 1,723,726.9307 median insert size = 249 >>>>>>> Mapping quality mean mapping quality = 54.9304 >>>>>>> ACTG content number of A's = 454,360,550 bp (27.96%) number of C's = 360,623,586 bp (22.19%) number of T's = 451,856,886 bp (27.8%) number of G's = 358,036,486 bp (22.03%) number of N's = 250,989 bp (0.02%) GC percentage = 44.22% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 10,274,257 number of insertions = 91,116 mapped reads with insertion percentage = 0.55% number of deletions = 89,347 mapped reads with deletion percentage = 0.53% homopolymer indels = 44.51% >>>>>>> Coverage mean coverageData = 0.525X std coverageData = 17.0249X There is a 5.3% of reference with a coverageData >= 1X There is a 2.34% of reference with a coverageData >= 2X There is a 1.03% of reference with a coverageData >= 3X There is a 0.72% of reference with a coverageData >= 4X There is a 0.52% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 152454022 0.611649517214242 22.32182324583913 chr2 243199373 90794375 0.37333309654544217 11.089730922699054 chr3 198022430 185252860 0.9355145273189507 21.1958148210038 chr4 191154276 59248830 0.30995294083821595 11.229633283334081 chr5 180915260 84224766 0.4655481577397064 14.95966018988492 chr6 171115067 109058890 0.6373424147389662 18.35539637510019 chr7 159138663 77162043 0.4848730129145298 14.402133645923008 chr8 146364022 108184931 0.7391497549855524 22.341179216617387 chr9 141213431 110992799 0.7859932175998188 20.180986962430648 chr10 135534747 40630444 0.29977880137261037 12.635942540591772 chr11 135006516 69376668 0.5138764413415423 17.789391531010565 chr12 133851895 96848534 0.7235499654300748 20.69735134883655 chr13 115169878 42731367 0.37102902027906987 13.158069414414923 chr14 107349540 53135289 0.49497453831660576 27.959868825416347 chr15 102531392 45519478 0.4439565006588421 13.282572858769027 chr16 90354753 52619394 0.5823644274695765 16.19975758551179 chr17 81195210 52705996 0.6491269127821703 14.701783509820991 chr18 78077248 31132847 0.3987441642410347 14.591122346597844 chr19 59128983 29410567 0.4973968011592555 11.615737900451558 chr20 63025520 29017369 0.4604066574936629 13.417766323791334 chr21 48129895 5536642 0.11503540574937884 4.407431349911128 chr22 51304566 13843934 0.2698382440268572 10.631146390599586 chrMT 16571 1465 0.08840745881359001 0.33927822525088186 chrX 155270560 82776741 0.533112915932035 16.163967289730515 chrY 59373566 2695992 0.04540727771008398 1.3908716124630522