BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082976.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 = 3,255,716 number of mapped reads = 2,635,694 (80.96%) number of supplementary alignments = 24,668 (0.76%) number of secondary alignments = 0 number of mapped bases = 173,902,312 bp number of sequenced bases = 173,832,795 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 106,485 duplication rate = 3.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8032 >>>>>>> ACTG content number of A's = 49,672,676 bp (28.57%) number of C's = 31,708,309 bp (18.24%) number of T's = 54,809,142 bp (31.53%) number of G's = 37,626,007 bp (21.64%) number of N's = 16,661 bp (0.01%) GC percentage = 39.89% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 1,623,998 number of insertions = 14,904 mapped reads with insertion percentage = 0.56% number of deletions = 40,110 mapped reads with deletion percentage = 1.51% homopolymer indels = 47.48% >>>>>>> Coverage mean coverageData = 0.0562X std coverageData = 0.405X There is a 4.71% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 15911828 0.06383866943304427 0.55771836523973 chr2 243199373 16209372 0.06665055012292322 0.5500919172284716 chr3 198022430 10784323 0.054460108382671596 0.2670612492068784 chr4 191154276 11042648 0.05776824997626524 0.28038060290832817 chr5 180915260 9457670 0.05227679522446033 0.2630574816368562 chr6 171115067 12938776 0.07561447525833596 0.43633032659154386 chr7 159138663 8968661 0.056357523878405334 0.47189917171268864 chr8 146364022 15588558 0.10650539515783462 0.5840129001170442 chr9 141213431 5066126 0.0358756668124578 0.37688520435757156 chr10 135534747 7816981 0.05767510673849563 0.3482159773611667 chr11 135006516 6942153 0.051420873641387796 0.3544199606544508 chr12 133851895 5093640 0.038054298745639724 0.22692441351160036 chr13 115169878 3522358 0.03058402128375963 0.20000980839655041 chr14 107349540 3401779 0.031688808354465234 0.22995628481446034 chr15 102531392 3424299 0.033397566669142655 0.20924631904762053 chr16 90354753 6997599 0.07744583176493217 0.36542492623074196 chr17 81195210 4946318 0.060918839916788196 0.35664377743388614 chr18 78077248 5805052 0.07435011029077254 0.8527035519282936 chr19 59128983 2387366 0.04037556336796796 0.4193520845737798 chr20 63025520 4099672 0.0650478092049062 0.30496984565794644 chr21 48129895 3625529 0.07532800559818383 0.32568481945931843 chr22 51304566 2916362 0.05684410233584278 0.2753750354657951 chrMT 16571 211177 12.74376923541126 8.448825111416566 chrX 155270560 6457546 0.04158899149974084 0.2773906453906509 chrY 59373566 286519 0.004825699706162166 0.09757168939203169