BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472587.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 7,727,014 number of mapped reads = 7,046,243 (91.19%) number of supplementary alignments = 191,453 (2.48%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,550,883 number of mapped paired reads (second in pair) = 3,495,360 number of mapped paired reads (both in pair) = 6,894,858 number of mapped paired reads (singletons) = 151,385 number of mapped bases = 571,583,295 bp number of sequenced bases = 571,351,851 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,071,523 duplication rate = 13.89% >>>>>>> Insert size mean insert size = 205,844.4222 std insert size = 4,465,227.8754 median insert size = 124 >>>>>>> Mapping quality mean mapping quality = 50.7988 >>>>>>> ACTG content number of A's = 145,987,165 bp (25.55%) number of C's = 115,858,264 bp (20.28%) number of T's = 168,353,663 bp (29.47%) number of G's = 140,766,518 bp (24.64%) number of N's = 386,241 bp (0.07%) GC percentage = 44.92% >>>>>>> Mismatches and indels general error rate = 0.0116 number of mismatches = 6,529,370 number of insertions = 51,172 mapped reads with insertion percentage = 0.71% number of deletions = 124,089 mapped reads with deletion percentage = 1.73% homopolymer indels = 43.12% >>>>>>> Coverage mean coverageData = 0.1846X std coverageData = 1.6239X There is a 10.15% of reference with a coverageData >= 1X There is a 4.71% of reference with a coverageData >= 2X There is a 1.62% of reference with a coverageData >= 3X There is a 0.79% of reference with a coverageData >= 4X There is a 0.36% of reference with a coverageData >= 5X There is a 0.2% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% 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% 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 49177615 0.19730187552872736 1.9855912323936644 chr2 243199373 48799516 0.2006564219226009 1.3808429094777033 chr3 198022430 38805488 0.19596511364899422 0.6891470268324912 chr4 191154276 35119678 0.18372426050254823 0.8531630864308244 chr5 180915260 34415871 0.19023199590791845 0.6930799423396862 chr6 171115067 34340582 0.20068707333644675 0.9402124992802247 chr7 159138663 30154691 0.18948689420621814 1.851655980283778 chr8 146364022 28096838 0.1919654681257666 1.114544530132312 chr9 141213431 24776964 0.17545755969911955 1.511647739580948 chr10 135534747 27727912 0.20458157493738488 1.3026701137516445 chr11 135006516 26161753 0.1937814097802509 1.2005895197480263 chr12 133851895 27869159 0.20820892375113553 0.7270763818938981 chr13 115169878 16660294 0.14465843230293254 0.5872736170048762 chr14 107349540 18968574 0.17669916424420637 5.76114302722678 chr15 102531392 18066263 0.1762022600844042 0.6651810150223241 chr16 90354753 18605466 0.20591574192007364 0.8660213777482721 chr17 81195210 18883710 0.23257172436649895 1.0433864763929328 chr18 78077248 15094366 0.19332605063129274 2.629564008732482 chr19 59128983 11558507 0.19547955018945615 1.3780037734439305 chr20 63025520 13670885 0.21691030871304195 1.211271956401146 chr21 48129895 6685694 0.13890938261967953 0.7057529848977864 chr22 51304566 7551155 0.14718290375948215 0.747433102894036 chrMT 16571 8711 0.5256773882083158 1.2713625927136292 chrX 155270560 16817107 0.10830840695106658 0.6756027900201255 chrY 59373566 3566496 0.06006875180783314 0.6426176919758931