BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124967.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 5,893,060 number of mapped reads = 5,734,020 (97.3%) number of supplementary alignments = 57,284 (0.97%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,873,012 number of mapped paired reads (second in pair) = 2,861,008 number of mapped paired reads (both in pair) = 5,702,606 number of mapped paired reads (singletons) = 31,414 number of mapped bases = 482,127,806 bp number of sequenced bases = 481,839,887 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 767,797 duplication rate = 9.63% >>>>>>> Insert size mean insert size = 81,513.4547 std insert size = 2,673,167.4664 median insert size = 161 >>>>>>> Mapping quality mean mapping quality = 52.3169 >>>>>>> ACTG content number of A's = 139,798,139 bp (29.01%) number of C's = 87,684,459 bp (18.2%) number of T's = 146,579,592 bp (30.42%) number of G's = 107,772,874 bp (22.37%) number of N's = 4,823 bp (0%) GC percentage = 40.56% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 3,707,292 number of insertions = 75,994 mapped reads with insertion percentage = 1.28% number of deletions = 152,856 mapped reads with deletion percentage = 2.61% homopolymer indels = 45.65% >>>>>>> Coverage mean coverageData = 0.1557X std coverageData = 2.2235X There is a 9.98% of reference with a coverageData >= 1X There is a 3.12% of reference with a coverageData >= 2X There is a 0.87% of reference with a coverageData >= 3X There is a 0.36% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% 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% 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 38188119 0.15321173061390286 1.7868375769708853 chr2 243199373 45309833 0.18630735943550314 2.3205535312697876 chr3 198022430 33726946 0.17031881691382134 0.6543328703034873 chr4 191154276 27613860 0.14445850010700256 1.7139275871476851 chr5 180915260 25967449 0.14353376824044584 0.5526303325077155 chr6 171115067 28761767 0.1680843627872933 1.0435437358977788 chr7 159138663 28440702 0.1787164819903005 1.5322602353626138 chr8 146364022 28282928 0.19323688713610235 0.842830246624788 chr9 141213431 18620660 0.13186181985763096 1.732027018120385 chr10 135534747 27976797 0.20641789370809835 8.009442199854812 chr11 135006516 20312696 0.15045715274957544 0.9278301378078554 chr12 133851895 22302244 0.16661881402575585 0.5624043509851515 chr13 115169878 14620731 0.126949261854736 0.4780092138554962 chr14 107349540 17893491 0.16668437517291643 0.6440193712870527 chr15 102531392 12700748 0.12387179918517052 0.5064880964009537 chr16 90354753 15333357 0.1697017200633596 3.1241940293887898 chr17 81195210 10013106 0.12332138804739837 1.4245794577639823 chr18 78077248 8847247 0.11331402203110437 1.9398167126535881 chr19 59128983 6738131 0.11395648391246642 1.1266260949516018 chr20 63025520 9337550 0.14815506480549467 0.687692495611338 chr21 48129895 5088994 0.10573457515334285 0.9548763460416344 chr22 51304566 3708286 0.07227984347436055 0.4266554407864848 chrMT 16571 210101 12.67883652163418 8.38246827728617 chrX 155270560 22537351 0.1451489000876921 0.7434393104724877 chrY 59373566 9594712 0.16159905234595476 3.8281440621944753