BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975235.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 3,696,052 number of mapped reads = 3,658,966 (99%) number of supplementary alignments = 38,018 (1.03%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,828,622 number of mapped paired reads (second in pair) = 1,830,344 number of mapped paired reads (both in pair) = 3,645,860 number of mapped paired reads (singletons) = 13,106 number of mapped bases = 342,550,917 bp number of sequenced bases = 342,319,912 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 203,992 duplication rate = 3.37% >>>>>>> Insert size mean insert size = 138,383.1451 std insert size = 3,550,960 median insert size = 175 >>>>>>> Mapping quality mean mapping quality = 52.7265 >>>>>>> ACTG content number of A's = 98,490,037 bp (28.77%) number of C's = 69,443,972 bp (20.29%) number of T's = 101,059,866 bp (29.52%) number of G's = 73,321,643 bp (21.42%) number of N's = 4,394 bp (0%) GC percentage = 41.71% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 2,937,189 number of insertions = 70,093 mapped reads with insertion percentage = 1.86% number of deletions = 131,920 mapped reads with deletion percentage = 3.52% homopolymer indels = 45.75% >>>>>>> Coverage mean coverageData = 0.1107X std coverageData = 1.0648X There is a 7.73% of reference with a coverageData >= 1X There is a 2.14% of reference with a coverageData >= 2X There is a 0.49% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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% 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 23326875 0.09358803162219603 1.3727360501018049 chr2 243199373 33664628 0.13842399174277475 1.6058206514209217 chr3 198022430 21080876 0.1064570109557791 0.4216600851828273 chr4 191154276 17103024 0.08947235896517429 0.8819049277968242 chr5 180915260 20344448 0.11245291303784988 0.44918927149495697 chr6 171115067 16353193 0.09556839901187661 0.5368863304470718 chr7 159138663 16261125 0.10218211397188878 0.9669176314959043 chr8 146364022 21423289 0.14636991186262974 0.6027552540299412 chr9 141213431 15254347 0.1080233437568697 1.4713548226580764 chr10 135534747 16718619 0.1233530099849598 2.068000320299241 chr11 135006516 19927645 0.14760506078091815 0.805937823855184 chr12 133851895 18392784 0.13741145764129825 0.477881096841012 chr13 115169878 8129208 0.07058449779724521 0.3299555492894999 chr14 107349540 11973121 0.11153397583259322 0.46365292449287765 chr15 102531392 7377237 0.07195100794106063 0.3358006635996484 chr16 90354753 9509684 0.10524829833799668 1.4479058297921628 chr17 81195210 9953195 0.12258352432366391 1.8419312391562295 chr18 78077248 8892178 0.1138894905722087 1.372086998580924 chr19 59128983 5915330 0.1000411253479533 0.7020140251326846 chr20 63025520 19044511 0.30217142198906094 0.7755403096888058 chr21 48129895 3416171 0.07097815193654589 0.47069695189663696 chr22 51304566 3177808 0.06194006202099049 0.34170562343522554 chrMT 16571 170993 10.318809969223341 5.260336413865729 chrX 155270560 9741883 0.06274134001964056 0.40798403075675826 chrY 59373566 5398745 0.09092842764404617 1.6563310637138755