BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617494.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 6,155,330 number of mapped reads = 5,753,278 (93.47%) number of supplementary alignments = 30,843 (0.5%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,907,277 number of mapped paired reads (second in pair) = 2,846,001 number of mapped paired reads (both in pair) = 5,622,030 number of mapped paired reads (singletons) = 131,248 number of mapped bases = 555,571,945 bp number of sequenced bases = 555,247,389 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 536,399 duplication rate = 5.6% >>>>>>> Insert size mean insert size = 39,650.7024 std insert size = 1,859,986.9602 median insert size = 214 >>>>>>> Mapping quality mean mapping quality = 52.6109 >>>>>>> ACTG content number of A's = 164,309,787 bp (29.59%) number of C's = 111,948,455 bp (20.16%) number of T's = 163,858,259 bp (29.51%) number of G's = 114,563,823 bp (20.63%) number of N's = 567,065 bp (0.1%) GC percentage = 40.79% >>>>>>> Mismatches and indels general error rate = 0.014 number of mismatches = 7,586,802 number of insertions = 82,833 mapped reads with insertion percentage = 1.41% number of deletions = 191,226 mapped reads with deletion percentage = 3.25% homopolymer indels = 47.54% >>>>>>> Coverage mean coverageData = 0.1795X std coverageData = 1.8542X There is a 12.57% of reference with a coverageData >= 1X There is a 3.17% of reference with a coverageData >= 2X There is a 0.85% of reference with a coverageData >= 3X There is a 0.29% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% 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 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 35725682 0.14333236906960403 1.7999597370982112 chr2 243199373 57545251 0.23661759604947666 2.1641565402811174 chr3 198022430 45815067 0.23136301781570906 0.6251365967534138 chr4 191154276 28682092 0.15004682395909366 1.1864910153885415 chr5 180915260 35716418 0.1974207040356905 0.581855521890179 chr6 171115067 26319929 0.1538142108783442 1.1290048117018217 chr7 159138663 42835534 0.2691711315935839 2.4830594202171214 chr8 146364022 24725847 0.16893391328095644 0.8330472576087742 chr9 141213431 23006980 0.16292345449775242 3.424806502926365 chr10 135534747 23507543 0.1734429253038706 3.5418488743202294 chr11 135006516 31297473 0.23182194406083334 2.3785891786856457 chr12 133851895 24174560 0.18060678184645798 0.5540179372895636 chr13 115169878 23591555 0.20484136485757154 0.5937660401950738 chr14 107349540 16172934 0.15065676108160314 0.5570014046137527 chr15 102531392 12438500 0.12131406545226656 0.4374352087142009 chr16 90354753 15103492 0.16715769230203087 2.8793066674085535 chr17 81195210 15502170 0.19092468632078174 2.573534819918174 chr18 78077248 9898747 0.12678145367008836 3.117881682411847 chr19 59128983 6607028 0.11173924638615888 1.1361397269007871 chr20 63025520 16216441 0.2572995986387736 0.713966942859562 chr21 48129895 8012634 0.16647935758014848 0.8048637785563099 chr22 51304566 4091570 0.07975060153515381 0.3585059042226487 chrMT 16571 395038 23.839116528875746 17.273549009211102 chrX 155270560 26241265 0.16900348011883257 0.8924317737176296 chrY 59373566 1948195 0.032812497736787447 2.5836013564204547