BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365354.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 582,080,132 number of mapped reads = 562,301,320 (96.6%) number of supplementary alignments = 2,519,559 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 281,701,249 number of mapped paired reads (second in pair) = 280,600,071 number of mapped paired reads (both in pair) = 559,802,970 number of mapped paired reads (singletons) = 2,498,350 number of mapped bases = 58,835,513,619 bp number of sequenced bases = 58,815,530,383 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 314,164,536 duplication rate = 30.71% >>>>>>> Insert size mean insert size = 58,840.1506 std insert size = 2,351,195.4577 median insert size = 162 >>>>>>> Mapping quality mean mapping quality = 53.8197 >>>>>>> ACTG content number of A's = 17,813,618,761 bp (30.29%) number of C's = 11,413,601,045 bp (19.41%) number of T's = 17,347,908,706 bp (29.5%) number of G's = 12,233,005,111 bp (20.8%) number of N's = 7,396,760 bp (0.01%) GC percentage = 40.2% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 305,741,260 number of insertions = 17,860,433 mapped reads with insertion percentage = 3.1% number of deletions = 9,408,135 mapped reads with deletion percentage = 1.63% homopolymer indels = 50.42% >>>>>>> Coverage mean coverageData = 19.0056X std coverageData = 166.5791X There is a 88.49% of reference with a coverageData >= 1X There is a 86.66% of reference with a coverageData >= 2X There is a 84.12% of reference with a coverageData >= 3X There is a 81.82% of reference with a coverageData >= 4X There is a 79.07% of reference with a coverageData >= 5X There is a 76.48% of reference with a coverageData >= 6X There is a 73.59% of reference with a coverageData >= 7X There is a 70.81% of reference with a coverageData >= 8X There is a 67.86% of reference with a coverageData >= 9X There is a 65.02% of reference with a coverageData >= 10X There is a 62.07% of reference with a coverageData >= 11X There is a 59.24% of reference with a coverageData >= 12X There is a 56.37% of reference with a coverageData >= 13X There is a 53.61% of reference with a coverageData >= 14X There is a 50.85% of reference with a coverageData >= 15X There is a 48.22% of reference with a coverageData >= 16X There is a 45.61% of reference with a coverageData >= 17X There is a 43.13% of reference with a coverageData >= 18X There is a 40.7% of reference with a coverageData >= 19X There is a 38.4% of reference with a coverageData >= 20X There is a 36.15% of reference with a coverageData >= 21X There is a 34.03% of reference with a coverageData >= 22X There is a 31.98% of reference with a coverageData >= 23X There is a 30.04% of reference with a coverageData >= 24X There is a 28.17% of reference with a coverageData >= 25X There is a 26.42% of reference with a coverageData >= 26X There is a 24.74% of reference with a coverageData >= 27X There is a 23.16% of reference with a coverageData >= 28X There is a 21.66% of reference with a coverageData >= 29X There is a 20.25% of reference with a coverageData >= 30X There is a 18.91% of reference with a coverageData >= 31X There is a 17.65% of reference with a coverageData >= 32X There is a 16.47% of reference with a coverageData >= 33X There is a 15.36% of reference with a coverageData >= 34X There is a 14.31% of reference with a coverageData >= 35X There is a 13.34% of reference with a coverageData >= 36X There is a 12.42% of reference with a coverageData >= 37X There is a 11.56% of reference with a coverageData >= 38X There is a 10.76% of reference with a coverageData >= 39X There is a 10.01% of reference with a coverageData >= 40X There is a 9.31% of reference with a coverageData >= 41X There is a 8.66% of reference with a coverageData >= 42X There is a 8.05% of reference with a coverageData >= 43X There is a 7.49% of reference with a coverageData >= 44X There is a 6.96% of reference with a coverageData >= 45X There is a 6.47% of reference with a coverageData >= 46X There is a 6.01% of reference with a coverageData >= 47X There is a 5.59% of reference with a coverageData >= 48X There is a 5.19% of reference with a coverageData >= 49X There is a 4.83% of reference with a coverageData >= 50X There is a 4.49% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4804603764 19.27619576121337 434.1030281879524 chr2 243199373 4989510567 20.516132527200224 102.01419612462162 chr3 198022430 4074057839 20.573719042837723 27.60218920408057 chr4 191154276 4197235556 21.957319730582434 113.64956931324035 chr5 180915260 3759950434 20.78293690648318 20.51603634193797 chr6 171115067 3538781588 20.680712984789352 81.67282792930291 chr7 159138663 3246756396 20.40205902697574 118.32202016109935 chr8 146364022 3075730843 21.014254739460494 53.663774339227075 chr9 141213431 2467327510 17.47232888916919 134.91705734538633 chr10 135534747 3035606062 22.39725331836861 331.14407881175214 chr11 135006516 2715655284 20.114994182947438 109.20391971735212 chr12 133851895 2679491256 20.01832888507107 36.66236338410182 chr13 115169878 2008823718 17.4422666141923 16.954813333360796 chr14 107349540 1771056400 16.49803436512164 19.95220624873106 chr15 102531392 1594951192 15.555735281541871 22.697738824194467 chr16 90354753 1636506133 18.112009370442305 58.52549669042831 chr17 81195210 1533165207 18.882458792827805 105.4527918226533 chr18 78077248 1673948789 21.439648961500282 175.20885883953602 chr19 59128983 1036155776 17.523652926687408 220.72770603613634 chr20 63025520 1190145573 18.88355023488898 35.60293720979983 chr21 48129895 823281812 17.105414670029926 70.60177032119468 chr22 51304566 651935624 12.70716575206971 60.44613502993591 chrMT 16571 51361213 3099.463701647456 543.5050518086467 chrX 155270560 1666146355 10.730600540115267 45.017648454381856 chrY 59373566 613328728 10.329996483620336 227.04991513459927