BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085104.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 = 1,657,397 number of mapped reads = 1,304,478 (78.71%) number of supplementary alignments = 6,691 (0.4%) number of secondary alignments = 0 number of mapped bases = 81,860,218 bp number of sequenced bases = 81,832,295 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,595 duplication rate = 1.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6471 >>>>>>> ACTG content number of A's = 24,362,905 bp (29.77%) number of C's = 15,639,125 bp (19.11%) number of T's = 23,612,713 bp (28.86%) number of G's = 18,215,911 bp (22.26%) number of N's = 1,641 bp (0%) GC percentage = 41.37% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 747,292 number of insertions = 6,699 mapped reads with insertion percentage = 0.51% number of deletions = 17,105 mapped reads with deletion percentage = 1.29% homopolymer indels = 45.42% >>>>>>> Coverage mean coverageData = 0.0264X std coverageData = 0.2267X There is a 2.42% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.02% 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 7651076 0.030696316700450667 0.3268546642094913 chr2 243199373 7344195 0.030198248085121504 0.25580214459013995 chr3 198022430 4997311 0.02523608562928957 0.17350098825473648 chr4 191154276 4558972 0.023849699286873395 0.17396606611396434 chr5 180915260 4380179 0.024211219108880036 0.16552793364497778 chr6 171115067 5847856 0.034174991732317764 0.23588148368700962 chr7 159138663 7735414 0.04860801174382117 0.2682257248342398 chr8 146364022 5054589 0.03453436801565893 0.31143092798968924 chr9 141213431 2653560 0.018791130427246682 0.2005105946386527 chr10 135534747 5617875 0.04144970293116052 0.35680652645368977 chr11 135006516 3312739 0.024537623058134467 0.20378399713248416 chr12 133851895 3605148 0.02693385850084528 0.17719398338709036 chr13 115169878 1302441 0.01130886845256535 0.1114284085841362 chr14 107349540 2723196 0.025367560960205326 0.1758719085512052 chr15 102531392 1371324 0.0133746745582075 0.12202815654806759 chr16 90354753 2152020 0.023817452082459903 0.1768558864912941 chr17 81195210 1361757 0.016771395751054772 0.15245206739932446 chr18 78077248 1762228 0.022570313953688532 0.3235944973422552 chr19 59128983 1330488 0.022501452460293458 0.2401562870018762 chr20 63025520 1867695 0.029633948279998323 0.1859271538524719 chr21 48129895 891983 0.018532826635088234 0.15729829403524098 chr22 51304566 614887 0.01198503462635275 0.11572734912201765 chrMT 16571 3059 0.18459960171383744 0.5230594175418417 chrX 155270560 3521279 0.02267834288740892 0.17140231341577364 chrY 59373566 198947 0.0033507672421090556 0.0892590804499711