BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708608.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 5,105,243 number of mapped reads = 5,012,696 (98.19%) number of supplementary alignments = 145 (0%) number of secondary alignments = 0 number of mapped bases = 250,007,742 bp number of sequenced bases = 249,985,978 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,748 duplication rate = 0.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7471 >>>>>>> ACTG content number of A's = 77,381,772 bp (30.95%) number of C's = 47,463,674 bp (18.99%) number of T's = 77,081,627 bp (30.83%) number of G's = 48,049,406 bp (19.22%) number of N's = 9,499 bp (0%) GC percentage = 38.21% >>>>>>> Mismatches and indels general error rate = 0.0016 number of mismatches = 369,196 number of insertions = 15,428 mapped reads with insertion percentage = 0.31% number of deletions = 12,715 mapped reads with deletion percentage = 0.25% homopolymer indels = 48.62% >>>>>>> Coverage mean coverageData = 0.0808X std coverageData = 0.2963X There is a 7.46% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.04% 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 19228972 0.0771471377798493 0.29269490109073937 chr2 243199373 22641151 0.09309707800932529 0.32035191365551346 chr3 198022430 18800415 0.09494083574269845 0.3187848967171821 chr4 191154276 19572553 0.10239139510538597 0.3309681193611738 chr5 180915260 17921029 0.09905758640813384 0.32570151030818045 chr6 171115067 16565420 0.0968086580008761 0.3224727484665225 chr7 159138663 13985101 0.0878799704381078 0.3083967234973593 chr8 146364022 13589051 0.09284420320179504 0.31548736076429296 chr9 141213431 10125657 0.07170463126839542 0.2790150185535809 chr10 135534747 10013008 0.07387779312414992 0.2812568410820789 chr11 135006516 11381517 0.08430346428612379 0.3025167933723134 chr12 133851895 11649496 0.08703273121385394 0.30657056103150065 chr13 115169878 9470017 0.08222650891407561 0.2986017045171473 chr14 107349540 7793911 0.07260311502033451 0.2812936739373605 chr15 102531392 6721286 0.06555344532921195 0.2679574043901484 chr16 90354753 4448690 0.04923581607267522 0.23052336683542857 chr17 81195210 4061457 0.050020894089688295 0.23277391150555674 chr18 78077248 7016809 0.08987008609729687 0.3097320151210387 chr19 59128983 2035937 0.03443213288481556 0.191354760791505 chr20 63025520 4005624 0.06355558827598726 0.2625386249279055 chr21 48129895 2987524 0.062072107159178304 0.26174851324296555 chr22 51304566 1428677 0.027846975647352713 0.1731936197256714 chrMT 16571 281 0.016957335103494058 0.12911151726194633 chrX 155270560 14230627 0.09165051636317921 0.3143314717594822 chrY 59373566 333532 0.00561751672453024 0.0787645772519959