BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038403.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 18,103,366 number of mapped reads = 16,907,169 (93.39%) number of supplementary alignments = 306,529 (1.69%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,609,673 number of mapped paired reads (second in pair) = 8,297,496 number of mapped paired reads (both in pair) = 16,510,012 number of mapped paired reads (singletons) = 397,157 number of mapped bases = 2,224,154,035 bp number of sequenced bases = 2,222,693,819 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,362,717 duplication rate = 17.93% >>>>>>> Insert size mean insert size = 84,782.4197 std insert size = 2,751,593.4132 median insert size = 230 >>>>>>> Mapping quality mean mapping quality = 53.1041 >>>>>>> ACTG content number of A's = 646,559,584 bp (29.09%) number of C's = 419,668,436 bp (18.88%) number of T's = 665,973,455 bp (29.96%) number of G's = 490,320,637 bp (22.06%) number of N's = 171,707 bp (0.01%) GC percentage = 40.94% >>>>>>> Mismatches and indels general error rate = 0.0133 number of mismatches = 28,578,915 number of insertions = 394,448 mapped reads with insertion percentage = 2.23% number of deletions = 735,166 mapped reads with deletion percentage = 4.2% homopolymer indels = 47.9% >>>>>>> Coverage mean coverageData = 0.7185X std coverageData = 10.338X There is a 22.82% of reference with a coverageData >= 1X There is a 14.25% of reference with a coverageData >= 2X There is a 8.78% of reference with a coverageData >= 3X There is a 6% of reference with a coverageData >= 4X There is a 4.06% of reference with a coverageData >= 5X There is a 2.89% of reference with a coverageData >= 6X There is a 2.06% of reference with a coverageData >= 7X There is a 1.52% of reference with a coverageData >= 8X There is a 1.13% of reference with a coverageData >= 9X There is a 0.85% of reference with a coverageData >= 10X There is a 0.65% of reference with a coverageData >= 11X There is a 0.5% of reference with a coverageData >= 12X There is a 0.4% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.2% of reference with a coverageData >= 16X There is a 0.17% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.08% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 189855294 0.7617043971176305 12.500825118660934 chr2 243199373 184352572 0.7580306220608554 14.141112129918492 chr3 198022430 158295019 0.7993792369884563 2.1436840614882455 chr4 191154276 101799230 0.5325501062816926 9.49971232321076 chr5 180915260 162129912 0.8961649337927602 2.244152554240488 chr6 171115067 136115257 0.7954603845609926 8.9989445186972 chr7 159138663 112808431 0.7088687869647365 11.405784355302632 chr8 146364022 145194401 0.9920088216761357 4.766324297097225 chr9 141213431 96213539 0.6813341926378094 17.7907920460187 chr10 135534747 120661077 0.8902593590999952 24.770943600994624 chr11 135006516 112831251 0.8357467057367809 8.915018700153636 chr12 133851895 93660930 0.6997355547338348 2.061813661883291 chr13 115169878 79188391 0.6875790126303685 1.8618556336519765 chr14 107349540 72826644 0.6784066703965382 2.0151594415138927 chr15 102531392 41938452 0.4090303582340909 1.402009900751894 chr16 90354753 63867124 0.7068485262750925 8.677685081443475 chr17 81195210 51223153 0.6308642221628591 10.546276900819255 chr18 78077248 96839560 1.2403044738462092 13.998455344346176 chr19 59128983 28047973 0.4743523662498981 5.9988204493742545 chr20 63025520 53460457 0.8482350800120332 3.6730333319894957 chr21 48129895 21626595 0.4493380881051164 4.507586075902239 chr22 51304566 10693640 0.20843446955578965 1.2398312689039501 chrMT 16571 6161527 371.8259006698449 337.00100927043 chrX 155270560 79643474 0.5129335142476462 2.3699154448300277 chrY 59373566 4720132 0.07949888002347712 9.880604452557199