BamQC report ----------------------------------- >>>>>>> Input bam file = SRR620537.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP016866/SRP016866.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 = 16,692,094 number of mapped reads = 8,242,821 (49.38%) number of supplementary alignments = 396 (0%) number of secondary alignments = 0 number of mapped bases = 372,164,472 bp number of sequenced bases = 372,077,456 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 697,408 duplication rate = 3.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 36.1338 >>>>>>> ACTG content number of A's = 93,971,993 bp (25.26%) number of C's = 78,702,036 bp (21.15%) number of T's = 108,848,078 bp (29.25%) number of G's = 90,513,766 bp (24.33%) number of N's = 41,583 bp (0.01%) GC percentage = 45.48% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 2,648,892 number of insertions = 25,787 mapped reads with insertion percentage = 0.31% number of deletions = 58,282 mapped reads with deletion percentage = 0.68% homopolymer indels = 35.56% >>>>>>> Coverage mean coverageData = 0.1202X std coverageData = 1.3477X There is a 9.24% of reference with a coverageData >= 1X There is a 1.47% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.05% 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 0.03% 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 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% 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% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% 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 30114425 0.12081985946185467 1.8740821230219222 chr2 243199373 30461396 0.12525277357520162 1.6662015143604632 chr3 198022430 22762278 0.11494797836790509 1.2666089163675152 chr4 191154276 23793087 0.1244705977699395 1.4635660466562712 chr5 180915260 20708299 0.11446408113942406 0.5705037350595547 chr6 171115067 19893913 0.11626044011659126 0.7325616049869729 chr7 159138663 20502234 0.12883251381846786 1.3888632577188609 chr8 146364022 17680133 0.1207956214813501 0.9659045147809812 chr9 141213431 15391037 0.10899131117351012 0.9026413526093655 chr10 135534747 20699232 0.15272269626917148 3.2672985973291446 chr11 135006516 16552748 0.12260703031548492 1.1399816023354046 chr12 133851895 16875396 0.12607513700123557 0.6291423679497379 chr13 115169878 10372794 0.09006516443474916 0.6155297160525875 chr14 107349540 11142248 0.10379409171199057 0.6883262287861798 chr15 102531392 10795269 0.10528745186644886 0.6475205835002255 chr16 90354753 12903248 0.14280652175541889 0.9614926912849581 chr17 81195210 11996129 0.14774429427548744 0.8711448708011682 chr18 78077248 9093944 0.11647367489181996 1.7327576503672109 chr19 59128983 10368981 0.17536207243747115 1.6770078760024716 chr20 63025520 8408300 0.13341103730679255 0.7664617345901251 chr21 48129895 4784705 0.09941232990431415 0.8749663323039162 chr22 51304566 5281077 0.10293580887128058 0.6025853514733206 chrMT 16571 56054 3.3826564480115864 3.0596381855527417 chrX 155270560 19345847 0.1245944305217937 0.8353468578834511 chrY 59373566 2181698 0.03674527482482693 1.1238040162560017