BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548979.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 7,514,963 number of mapped reads = 3,321,565 (44.2%) number of secondary alignments = 0 number of mapped bases = 131,462,925 bp number of sequenced bases = 131,448,405 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 71,032 duplication rate = 1.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.106 >>>>>>> ACTG content number of A's = 38,648,594 bp (29.4%) number of C's = 26,693,553 bp (20.31%) number of T's = 39,084,230 bp (29.73%) number of G's = 27,014,853 bp (20.55%) number of N's = 7,175 bp (0.01%) GC percentage = 40.86% >>>>>>> Mismatches and indels general error rate = 0.0028 number of mismatches = 368,932 number of insertions = 4,418 mapped reads with insertion percentage = 0.13% number of deletions = 11,620 mapped reads with deletion percentage = 0.35% homopolymer indels = 44.7% >>>>>>> Coverage mean coverageData = 0.0425X std coverageData = 0.3039X There is a 3.76% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% 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 10551667 0.04233356353403027 0.4761955292291203 chr2 243199373 11179878 0.045970011608541445 0.3000073711860213 chr3 198022430 9041290 0.04565790855106666 0.23542490483610076 chr4 191154276 9301030 0.048657190383750555 0.24687667260790672 chr5 180915260 8381116 0.04632619713782021 0.238654600623151 chr6 171115067 8040427 0.04698842212416046 0.27024239265736993 chr7 159138663 7482912 0.04702133258465292 0.45130330311454575 chr8 146364022 6830291 0.04666646151606848 0.4078452750798826 chr9 141213431 5803282 0.04109582182731613 0.28112703368157077 chr10 135534747 6126350 0.04520132390847345 0.2660187975265978 chr11 135006516 5996437 0.044415908044023594 0.27702737562862534 chr12 133851895 6009739 0.044898422992068955 0.23814984947131115 chr13 115169878 4400861 0.03821190988845191 0.21441958935548414 chr14 107349540 4143117 0.03859464139296731 0.24454411930673725 chr15 102531392 3700406 0.03609046876102102 0.20892579570054715 chr16 90354753 3650593 0.04040288837931968 0.23208490095036965 chr17 81195210 3372735 0.04153859568809539 0.23993392649565448 chr18 78077248 3533395 0.04525511708609402 0.40625728432482233 chr19 59128983 2498754 0.04225937726681347 0.4219767201187175 chr20 63025520 2651722 0.04207378217585511 0.22959426889248893 chr21 48129895 1720643 0.03574998449508356 0.23093310776375378 chr22 51304566 1447473 0.02821333680125079 0.2204674137626871 chrMT 16571 631 0.0380785709975258 0.19697985533039672 chrX 155270560 4635522 0.029854481107043085 0.21907691744706415 chrY 59373566 962654 0.016213511581904986 0.1630443650004298