BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094094.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 808,670 number of mapped reads = 766,276 (94.76%) number of supplementary alignments = 54,540 (6.74%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 384,913 number of mapped paired reads (second in pair) = 381,363 number of mapped paired reads (both in pair) = 760,418 number of mapped paired reads (singletons) = 5,858 number of mapped bases = 92,054,765 bp number of sequenced bases = 90,246,668 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 766,082 duplication rate = 57.26% >>>>>>> Insert size mean insert size = 1,650,182.0234 std insert size = 11,518,092.608 median insert size = 135 >>>>>>> Mapping quality mean mapping quality = 40.1122 >>>>>>> ACTG content number of A's = 25,271,984 bp (28%) number of C's = 19,855,509 bp (22%) number of T's = 23,937,307 bp (26.52%) number of G's = 21,180,765 bp (23.47%) number of N's = 1,103 bp (0%) GC percentage = 45.47% >>>>>>> Mismatches and indels general error rate = 0.0354 number of mismatches = 3,078,137 number of insertions = 63,160 mapped reads with insertion percentage = 8.14% number of deletions = 242,256 mapped reads with deletion percentage = 30.66% homopolymer indels = 26.14% >>>>>>> Coverage mean coverageData = 0.0297X std coverageData = 7.1517X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2661576 0.010678312412308894 4.77160824700865 chr2 243199373 4715727 0.019390374826336414 7.461703931093692 chr3 198022430 1566355 0.007909987772597276 3.3893725342485497 chr4 191154276 5729758 0.029974521731337047 9.21498970330085 chr5 180915260 2413729 0.013341765642102274 6.199760940402123 chr6 171115067 2194541 0.012824943112695037 4.955960556521107 chr7 159138663 2795018 0.017563412607029382 5.51202944402147 chr8 146364022 1802307 0.012313866313403166 3.8157400557296017 chr9 141213431 1792765 0.012695428383154291 6.178397020991349 chr10 135534747 1159322 0.008553688450091695 2.800701928205935 chr11 135006516 3068455 0.022728199281877623 6.923291563925486 chr12 133851895 2902527 0.021684616418766428 5.4176104671318015 chr13 115169878 2505083 0.021751199562788457 6.656405645695987 chr14 107349540 533161 0.004966588585288768 1.7820594245660308 chr15 102531392 904791 0.008824526638631806 2.0723995115091824 chr16 90354753 457106 0.0050590144383439355 1.929882803565624 chr17 81195210 711846 0.00876709352682258 3.7656423518431326 chr18 78077248 323768 0.004146765008930643 1.1341976809592198 chr19 59128983 260215 0.004400802902360083 1.605639490429455 chr20 63025520 631531 0.010020242593793752 3.6304586949782864 chr21 48129895 321132 0.006672194069818768 2.2216550744668435 chr22 51304566 164791 0.0032120143068747526 1.2608042263202452 chrMT 16571 29031 1.75191599782753 10.175878165021837 chrX 155270560 51089616 0.32903607741222807 22.030875180174988 chrY 59373566 1320614 0.022242457190460817 4.9961143438921845