BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173887.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 1,213,654 number of mapped reads = 1,181,861 (97.38%) number of supplementary alignments = 130,081 (10.72%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 591,390 number of mapped paired reads (second in pair) = 590,471 number of mapped paired reads (both in pair) = 1,161,162 number of mapped paired reads (singletons) = 20,699 number of mapped bases = 139,429,783 bp number of sequenced bases = 139,347,196 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 887,050 duplication rate = 62.69% >>>>>>> Insert size mean insert size = 1,146,825.0591 std insert size = 9,753,982.686 median insert size = 196 >>>>>>> Mapping quality mean mapping quality = 52.7445 >>>>>>> ACTG content number of A's = 42,174,129 bp (30.27%) number of C's = 27,064,628 bp (19.42%) number of T's = 42,014,868 bp (30.15%) number of G's = 28,091,954 bp (20.16%) number of N's = 1,617 bp (0%) GC percentage = 39.58% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 1,435,299 number of insertions = 16,681 mapped reads with insertion percentage = 1.35% number of deletions = 33,264 mapped reads with deletion percentage = 2.75% homopolymer indels = 42.54% >>>>>>> Coverage mean coverageData = 0.045X std coverageData = 0.847X There is a 1.08% of reference with a coverageData >= 1X There is a 0.81% of reference with a coverageData >= 2X There is a 0.59% of reference with a coverageData >= 3X There is a 0.47% of reference with a coverageData >= 4X There is a 0.34% of reference with a coverageData >= 5X There is a 0.27% of reference with a coverageData >= 6X There is a 0.19% of reference with a coverageData >= 7X There is a 0.16% of reference with a coverageData >= 8X There is a 0.11% of reference with a coverageData >= 9X There is a 0.09% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% 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 10386711 0.04167175575462257 0.6796498173331935 chr2 243199373 11862480 0.04877677048945352 2.0967943616853266 chr3 198022430 9379221 0.04736443745286834 0.5993426578409097 chr4 191154276 8745262 0.04574975869229313 0.6780328109954556 chr5 180915260 8278655 0.04575984911388901 0.585836579597154 chr6 171115067 9182227 0.05366112500192634 0.6615191796618151 chr7 159138663 6556129 0.041197587540370374 0.6664930663578545 chr8 146364022 7357464 0.05026825513171536 0.7103007422774809 chr9 141213431 6145935 0.04352231198178309 0.644076162726377 chr10 135534747 5965245 0.04401266193384343 0.7240397062530727 chr11 135006516 6715647 0.04974313239814292 0.6218748071595088 chr12 133851895 7400060 0.05528543320212239 0.6354219299683169 chr13 115169878 5554833 0.048231647861952234 0.6100707504566779 chr14 107349540 4637761 0.043202430117539395 0.5674232388885871 chr15 102531392 4584148 0.04470970217589555 0.580427798089473 chr16 90354753 4469841 0.049469904477520955 0.6498974897158397 chr17 81195210 3986756 0.04910087676354307 0.6150410486676442 chr18 78077248 3750486 0.04803558137704853 0.8375272131170087 chr19 59128983 2567792 0.0434269603453183 0.6349149153650161 chr20 63025520 2760488 0.0437995275564565 0.5745490010892289 chr21 48129895 1988738 0.04132022311704607 0.6140829451189788 chr22 51304566 1671628 0.032582441102805546 0.48135685666245215 chrMT 16571 236345 14.26256713535695 12.97628899673356 chrX 155270560 4188313 0.026974289266426296 0.4479992712755957 chrY 59373566 1057618 0.01781294389493129 0.45210094545327867