BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124787.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 720,499 number of mapped reads = 719,535 (99.87%) number of supplementary alignments = 341,498 (47.4%) number of secondary alignments = 0 number of mapped bases = 107,310,418 bp number of sequenced bases = 107,279,762 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,045,830 duplication rate = 2.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.3234 >>>>>>> ACTG content number of A's = 29,783,129 bp (27.76%) number of C's = 18,418,785 bp (17.17%) number of T's = 36,547,676 bp (34.07%) number of G's = 22,530,172 bp (21%) number of N's = 0 bp (0%) GC percentage = 38.17% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 776,585 number of insertions = 5,808 mapped reads with insertion percentage = 0.8% number of deletions = 29,192 mapped reads with deletion percentage = 4.02% homopolymer indels = 54.19% >>>>>>> Coverage mean coverageData = 0.0347X std coverageData = 107.8328X There is a 0.06% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 1262526 0.005065287279665393 4.1863305682976435 chr2 243199373 169246 6.959146231022562E-4 0.04981640829751857 chr3 198022430 112084 5.660166881095237E-4 0.024047478587290356 chr4 191154276 114207 5.974598234987953E-4 0.03744893455305894 chr5 180915260 101315 5.600135665725489E-4 0.023900086672469168 chr6 171115067 114028 6.663819966245286E-4 0.05528054094682225 chr7 159138663 115568 7.262094441499738E-4 0.027662172016708682 chr8 146364022 97724 6.676777439198822E-4 0.03416897868925015 chr9 141213431 77387 5.480144448866199E-4 0.02432148973176181 chr10 135534747 104433196 0.7705271032822306 515.3208721195447 chr11 135006516 71454 5.29263343111528E-4 0.031517750565424975 chr12 133851895 80791 6.035850295582293E-4 0.024847106542279774 chr13 115169878 40403 3.5081221497864224E-4 0.018815513759826437 chr14 107349540 52638 4.903421104552474E-4 0.022301330011984064 chr15 102531392 50877 4.962090049455293E-4 0.022985512212159144 chr16 90354753 69446 7.685926605322024E-4 0.04248782052317636 chr17 81195210 55411 6.824417351713236E-4 0.027445166726026583 chr18 78077248 33695 4.315597803857021E-4 0.02120074332998262 chr19 59128983 62424 0.001055725920400153 0.16320371098701725 chr20 63025520 48726 7.731153983338813E-4 0.028356535146623566 chr21 48129895 19330 4.0162148701965796E-4 0.020418583579985133 chr22 51304566 25192 4.910284203554124E-4 0.03212759001902525 chrMT 16571 9058 0.5466175849375415 0.7774828498739672 chrX 155270560 63176 4.0687687350390183E-4 0.020408669209316416 chrY 59373566 30516 5.139660973033016E-4 0.031994169843460984