BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549007.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 = 9,327,537 number of mapped reads = 8,078,059 (86.6%) number of secondary alignments = 0 number of mapped bases = 320,583,459 bp number of sequenced bases = 320,546,655 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 647,759 duplication rate = 7.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7686 >>>>>>> ACTG content number of A's = 96,226,892 bp (30.02%) number of C's = 63,506,446 bp (19.81%) number of T's = 96,244,838 bp (30.03%) number of G's = 64,565,485 bp (20.14%) number of N's = 2,994 bp (0%) GC percentage = 39.95% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 967,007 number of insertions = 9,911 mapped reads with insertion percentage = 0.12% number of deletions = 28,459 mapped reads with deletion percentage = 0.35% homopolymer indels = 43.21% >>>>>>> Coverage mean coverageData = 0.1036X std coverageData = 0.787X There is a 7.9% of reference with a coverageData >= 1X There is a 1.73% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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% 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 25840984 0.10367470257977812 1.2312313093487421 chr2 243199373 27911488 0.11476792746501037 0.5803562175378638 chr3 198022430 22422788 0.11323357662058788 0.4147845792187649 chr4 191154276 22555568 0.117996669873082 0.4672569122381458 chr5 180915260 20722316 0.11454155940189899 0.42529146525091466 chr6 171115067 19620459 0.11466236926991356 0.49511170191947124 chr7 159138663 18148478 0.1140419157599684 0.8285210770561853 chr8 146364022 17099084 0.11682573194114602 2.2434508051140853 chr9 141213431 13503920 0.09562773104776415 0.5404222595100121 chr10 135534747 15068746 0.11117994708766454 0.6416587594505437 chr11 135006516 14823707 0.10979993736006045 0.5350926686312121 chr12 133851895 14912547 0.11141080221538888 0.4313857634703745 chr13 115169878 11099306 0.09637334164754434 0.3817053378166241 chr14 107349540 10199649 0.09501343927510075 0.4776754310575028 chr15 102531392 8997736 0.08775591381808218 0.36364546039425666 chr16 90354753 8470933 0.09375193577254315 0.4240125420885085 chr17 81195210 7590463 0.09348412301661638 0.41439559219251854 chr18 78077248 8759506 0.11219025035308622 1.0900098542038512 chr19 59128983 5344311 0.09038394927238982 0.9646800348834039 chr20 63025520 6280607 0.09965180771217755 0.4156979351665624 chr21 48129895 4281549 0.08895820362791151 0.4656296865050726 chr22 51304566 3101611 0.06045487257410968 0.33941451611931966 chrMT 16571 6165 0.37203548367630196 0.7263832915251864 chrX 155270560 10989817 0.07077849786849484 0.4108646661799867 chrY 59373566 2831721 0.047693295026274826 0.47840801411586964