BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081250.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,235,614 number of mapped reads = 1,916,427 (85.72%) number of supplementary alignments = 10,612 (0.47%) number of secondary alignments = 0 number of mapped bases = 128,165,645 bp number of sequenced bases = 128,107,602 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,430 duplication rate = 2.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4536 >>>>>>> ACTG content number of A's = 35,204,766 bp (27.48%) number of C's = 22,854,345 bp (17.84%) number of T's = 41,451,247 bp (32.36%) number of G's = 28,564,158 bp (22.3%) number of N's = 33,086 bp (0.03%) GC percentage = 40.14% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,104,259 number of insertions = 10,670 mapped reads with insertion percentage = 0.55% number of deletions = 34,673 mapped reads with deletion percentage = 1.79% homopolymer indels = 50.07% >>>>>>> Coverage mean coverageData = 0.0414X std coverageData = 0.389X There is a 3.64% of reference with a coverageData >= 1X There is a 0.36% 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 0.01% 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 12798520 0.05134799644089954 0.7377269489922845 chr2 243199373 8010432 0.03293771649649771 0.4129858828304194 chr3 198022430 7974321 0.040269786609527014 0.2250307242003075 chr4 191154276 5732540 0.029989075420944283 0.20954430816474837 chr5 180915260 9300624 0.05140873135853769 0.25286980903768225 chr6 171115067 8789953 0.05136866761125132 0.3200742769056481 chr7 159138663 8187824 0.05145087840784486 0.5796410983724275 chr8 146364022 7868414 0.05375920866673095 0.4820817530246834 chr9 141213431 4467220 0.03163452632207485 0.3716534711977737 chr10 135534747 3964035 0.029247370786769537 0.35316147258696035 chr11 135006516 6640064 0.049183285346019893 0.3727420610862311 chr12 133851895 3452199 0.025791185100517255 0.18742299182510044 chr13 115169878 4243612 0.03684654419795426 0.20928542155030588 chr14 107349540 4563392 0.04250965584016476 0.2403841805981914 chr15 102531392 4130691 0.0402870859297414 0.2200990884027122 chr16 90354753 3972059 0.043960708962371906 0.24855472276335788 chr17 81195210 1986446 0.024465063887389418 0.20571414499312946 chr18 78077248 4116764 0.05272680717435123 0.6164538085462515 chr19 59128983 2993293 0.05062310982077943 0.5522223537665932 chr20 63025520 2864418 0.04544854211436891 0.2400195394996154 chr21 48129895 1989624 0.04133863163424728 0.24811115967799707 chr22 51304566 815437 0.015894043426856002 0.13502025740266338 chrMT 16571 57415 3.464787882445236 2.5538156852192615 chrX 155270560 8891371 0.05726372726420256 0.30062278428646205 chrY 59373566 354977 0.005978704395151202 0.1443278779431505