BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818982.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,375,765 number of mapped reads = 1,356,451 (98.6%) number of supplementary alignments = 18,300 (1.33%) number of secondary alignments = 0 number of mapped bases = 125,645,288 bp number of sequenced bases = 125,572,143 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 516,612 duplication rate = 32.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2109 >>>>>>> ACTG content number of A's = 36,433,707 bp (29.01%) number of C's = 28,217,824 bp (22.47%) number of T's = 34,510,919 bp (27.48%) number of G's = 26,403,354 bp (21.03%) number of N's = 6,339 bp (0.01%) GC percentage = 43.5% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 793,735 number of insertions = 18,794 mapped reads with insertion percentage = 1.34% number of deletions = 39,310 mapped reads with deletion percentage = 2.83% homopolymer indels = 41.6% >>>>>>> Coverage mean coverageData = 0.0406X std coverageData = 0.5102X There is a 2.18% of reference with a coverageData >= 1X There is a 0.9% of reference with a coverageData >= 2X There is a 0.43% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.11% 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 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 12642112 0.05072048346070119 0.8940457708553077 chr2 243199373 10425818 0.042869427956954476 0.6986276615222213 chr3 198022430 6841486 0.0345490457823389 0.3080968426743671 chr4 191154276 6715833 0.03513305137887682 0.34767546738630417 chr5 180915260 6905412 0.03816931750256999 0.3364650016786994 chr6 171115067 4714519 0.027551746802051042 0.3106143724391437 chr7 159138663 5859431 0.03681965708107024 0.5635634150411839 chr8 146364022 11586895 0.07916491253567766 0.5094791126090836 chr9 141213431 5578143 0.0395015046408723 0.47871545231148527 chr10 135534747 6624289 0.048875208362620104 0.632603843041194 chr11 135006516 3948361 0.029245706925730905 0.3216594777133551 chr12 133851895 5903606 0.04410550930190417 0.3564951256270799 chr13 115169878 2352526 0.020426573691429976 0.23549787121086702 chr14 107349540 2903694 0.027048965463661978 0.28177788652305724 chr15 102531392 3387247 0.03303619441741316 0.30194601181004393 chr16 90354753 4120468 0.04560322355150481 0.5814292796807145 chr17 81195210 4588480 0.056511708018243935 0.44292900849319256 chr18 78077248 3114888 0.03989495121549366 0.5303128272272448 chr19 59128983 2646334 0.044755276781946345 0.9017286000118392 chr20 63025520 3796961 0.060244818289480195 0.4354353698913647 chr21 48129895 1705451 0.035434338678694395 0.35575461897649396 chr22 51304566 1097248 0.02138694633924006 0.2631552098990841 chrMT 16571 10379 0.6263351638404442 1.15459217790005 chrX 155270560 7719716 0.04971783446907128 0.4073486503093327 chrY 59373566 455991 0.007680033905997831 0.4900304074246986