BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013231.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,405,869 number of mapped reads = 1,273,475 (90.58%) number of supplementary alignments = 5,970 (0.42%) number of secondary alignments = 0 number of mapped bases = 88,083,282 bp number of sequenced bases = 88,046,030 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,240 duplication rate = 2.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9739 >>>>>>> ACTG content number of A's = 25,163,771 bp (28.58%) number of C's = 16,165,628 bp (18.36%) number of T's = 28,322,045 bp (32.17%) number of G's = 18,375,252 bp (20.87%) number of N's = 19,334 bp (0.02%) GC percentage = 39.23% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 681,164 number of insertions = 6,676 mapped reads with insertion percentage = 0.52% number of deletions = 21,824 mapped reads with deletion percentage = 1.7% homopolymer indels = 47.42% >>>>>>> Coverage mean coverageData = 0.0285X std coverageData = 0.2631X There is a 2.49% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.04% 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 5991819 0.02403933428916111 0.3176512866070287 chr2 243199373 10833627 0.04454627849719004 0.3496337205201045 chr3 198022430 7487492 0.03781133278689692 0.21646543406964527 chr4 191154276 6604351 0.034549847056520984 0.20954904989660267 chr5 180915260 4029882 0.022274970060568687 0.165618031720945 chr6 171115067 6704189 0.03917941954228964 0.25254050782792165 chr7 159138663 5773358 0.03627878914629313 0.52441524809934 chr8 146364022 4327799 0.029568735136289163 0.3404538520009912 chr9 141213431 3906235 0.027661922611313085 0.22783739772347 chr10 135534747 3140064 0.023167962972624283 0.2438776553968281 chr11 135006516 3937077 0.029162125774729274 0.20642405378555267 chr12 133851895 4273442 0.031926645491272276 0.2000525440032835 chr13 115169878 1884976 0.01636691844025397 0.14291695375559202 chr14 107349540 3855237 0.035912934512807415 0.22139335181299746 chr15 102531392 1272043 0.012406375990681956 0.12353570094079079 chr16 90354753 1933889 0.021403290206548405 0.17493313818021675 chr17 81195210 2129265 0.026224022328410753 0.18204313765691515 chr18 78077248 2234644 0.028620937049420595 0.38433568288357045 chr19 59128983 1116736 0.01888644017435578 0.23841590980418967 chr20 63025520 1491511 0.02366519149703168 0.1724834929594577 chr21 48129895 1084244 0.022527454090643665 0.17042842479525028 chr22 51304566 887397 0.017296647631713714 0.14406473400841666 chrMT 16571 47542 2.8689879910687344 2.4005431392182315 chrX 155270560 3018865 0.0194426103699246 0.1616496733593466 chrY 59373566 117598 0.0019806457304585683 0.05563822791290117