BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708593.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 = 6,337,258 number of mapped reads = 6,023,838 (95.05%) number of supplementary alignments = 142 (0%) number of secondary alignments = 0 number of mapped bases = 300,487,487 bp number of sequenced bases = 300,461,643 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 61,374 duplication rate = 1.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6527 >>>>>>> ACTG content number of A's = 93,193,167 bp (31.02%) number of C's = 56,963,513 bp (18.96%) number of T's = 92,546,957 bp (30.8%) number of G's = 57,749,544 bp (19.22%) number of N's = 8,462 bp (0%) GC percentage = 38.18% >>>>>>> Mismatches and indels general error rate = 0.0015 number of mismatches = 429,495 number of insertions = 19,093 mapped reads with insertion percentage = 0.32% number of deletions = 15,216 mapped reads with deletion percentage = 0.25% homopolymer indels = 48.82% >>>>>>> Coverage mean coverageData = 0.0971X std coverageData = 0.3282X There is a 8.81% of reference with a coverageData >= 1X There is a 0.81% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.01% 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 25240086 0.10126388411285041 0.3382569762645617 chr2 243199373 27847374 0.11450430014060933 0.35456455866961917 chr3 198022430 23469835 0.11852109379730368 0.3602466329844453 chr4 191154276 24100698 0.12607982674685236 0.3713088946436422 chr5 180915260 22976893 0.12700362036900592 0.3725501939043588 chr6 171115067 21635883 0.1264405489202187 0.3725790473887662 chr7 159138663 15017857 0.09436963159606286 0.3232397024094722 chr8 146364022 13817301 0.09440367114262548 0.3215686650403618 chr9 141213431 11599845 0.08214406319466878 0.30216425618103365 chr10 135534747 12413845 0.09159160491884785 0.31673043083472263 chr11 135006516 14057528 0.10412481127947928 0.34019244048618336 chr12 133851895 13918820 0.10398672353499366 0.33900794642619514 chr13 115169878 12260840 0.10645873915052684 0.34394580928282537 chr14 107349540 7987287 0.07440448277654474 0.2869623018764948 chr15 102531392 8095787 0.07895910551960515 0.29803275643445065 chr16 90354753 4983460 0.0551543757747863 0.24582268167399257 chr17 81195210 5418322 0.06673203998117623 0.2734977646538536 chr18 78077248 8256731 0.10575079439275319 0.3392459641158138 chr19 59128983 2402735 0.04063548666142287 0.20943257317421357 chr20 63025520 4324082 0.06860843036281176 0.2749930776466278 chr21 48129895 3172593 0.06591730565794918 0.27097203539317405 chr22 51304566 1452691 0.028315043148401255 0.1743022423531171 chrMT 16571 150 0.009051958240299317 0.09471019106894038 chrX 155270560 15668567 0.10091138332984695 0.3332258874799589 chrY 59373566 368277 0.006202709805235549 0.08296284135730922