BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365350.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 = 534,193,354 number of mapped reads = 505,314,998 (94.59%) number of supplementary alignments = 2,168,592 (0.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 253,146,791 number of mapped paired reads (second in pair) = 252,168,207 number of mapped paired reads (both in pair) = 503,146,880 number of mapped paired reads (singletons) = 2,168,118 number of mapped bases = 53,402,739,272 bp number of sequenced bases = 53,384,919,166 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 274,907,690 duplication rate = 28.63% >>>>>>> Insert size mean insert size = 58,082.3866 std insert size = 2,350,422.4296 median insert size = 165 >>>>>>> Mapping quality mean mapping quality = 53.8377 >>>>>>> ACTG content number of A's = 16,057,097,071 bp (30.08%) number of C's = 10,475,142,020 bp (19.62%) number of T's = 15,685,195,438 bp (29.38%) number of G's = 11,161,050,464 bp (20.91%) number of N's = 6,434,173 bp (0.01%) GC percentage = 40.53% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 276,961,312 number of insertions = 15,759,663 mapped reads with insertion percentage = 3.05% number of deletions = 8,423,418 mapped reads with deletion percentage = 1.62% homopolymer indels = 50.44% >>>>>>> Coverage mean coverageData = 17.2507X std coverageData = 164.2905X There is a 83.89% of reference with a coverageData >= 1X There is a 81.34% of reference with a coverageData >= 2X There is a 78.18% of reference with a coverageData >= 3X There is a 75.5% of reference with a coverageData >= 4X There is a 72.45% of reference with a coverageData >= 5X There is a 69.67% of reference with a coverageData >= 6X There is a 66.65% of reference with a coverageData >= 7X There is a 63.84% of reference with a coverageData >= 8X There is a 60.89% of reference with a coverageData >= 9X There is a 58.13% of reference with a coverageData >= 10X There is a 55.28% of reference with a coverageData >= 11X There is a 52.61% of reference with a coverageData >= 12X There is a 49.91% of reference with a coverageData >= 13X There is a 47.36% of reference with a coverageData >= 14X There is a 44.82% of reference with a coverageData >= 15X There is a 42.44% of reference with a coverageData >= 16X There is a 40.08% of reference with a coverageData >= 17X There is a 37.87% of reference with a coverageData >= 18X There is a 35.71% of reference with a coverageData >= 19X There is a 33.68% of reference with a coverageData >= 20X There is a 31.71% of reference with a coverageData >= 21X There is a 29.86% of reference with a coverageData >= 22X There is a 28.08% of reference with a coverageData >= 23X There is a 26.41% of reference with a coverageData >= 24X There is a 24.8% of reference with a coverageData >= 25X There is a 23.3% of reference with a coverageData >= 26X There is a 21.86% of reference with a coverageData >= 27X There is a 20.52% of reference with a coverageData >= 28X There is a 19.23% of reference with a coverageData >= 29X There is a 18.04% of reference with a coverageData >= 30X There is a 16.89% of reference with a coverageData >= 31X There is a 15.83% of reference with a coverageData >= 32X There is a 14.81% of reference with a coverageData >= 33X There is a 13.87% of reference with a coverageData >= 34X There is a 12.97% of reference with a coverageData >= 35X There is a 12.14% of reference with a coverageData >= 36X There is a 11.35% of reference with a coverageData >= 37X There is a 10.61% of reference with a coverageData >= 38X There is a 9.92% of reference with a coverageData >= 39X There is a 9.27% of reference with a coverageData >= 40X There is a 8.66% of reference with a coverageData >= 41X There is a 8.09% of reference with a coverageData >= 42X There is a 7.55% of reference with a coverageData >= 43X There is a 7.06% of reference with a coverageData >= 44X There is a 6.59% of reference with a coverageData >= 45X There is a 6.15% of reference with a coverageData >= 46X There is a 5.75% of reference with a coverageData >= 47X There is a 5.37% of reference with a coverageData >= 48X There is a 5.01% of reference with a coverageData >= 49X There is a 4.68% of reference with a coverageData >= 50X There is a 4.37% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4450454652 17.855340276163243 435.83095621098846 chr2 243199373 4684370387 19.26144105231719 94.31013680377143 chr3 198022430 3645260314 18.408320279677408 27.911793578970848 chr4 191154276 3751218403 19.62403604824409 93.6443351324046 chr5 180915260 3199255431 17.683723479158143 20.114265431012612 chr6 171115067 3082229055 18.012610514303805 83.31577671794652 chr7 159138663 3046362454 19.142817946132926 108.22153942540218 chr8 146364022 2602229586 17.77916150732726 54.37830682741317 chr9 141213431 2222566731 15.739060479310924 126.92798793514018 chr10 135534747 2783399587 20.5364281013488 336.2569254681141 chr11 135006516 2505095946 18.555370660776106 105.47022187173053 chr12 133851895 2400678926 17.935337605791833 33.99017229170069 chr13 115169878 1680273426 14.589521628216017 16.234373378952153 chr14 107349540 1586213634 14.776156786512546 18.98443361366455 chr15 102531392 1564789625 15.2615661845301 21.76264914168402 chr16 90354753 1491170431 16.503508465127453 58.27849264779027 chr17 81195210 1847088546 22.74873783810646 99.94249501808697 chr18 78077248 1462247915 18.7282204797997 149.48510336059647 chr19 59128983 948245400 16.036896829427963 219.91879701782608 chr20 63025520 1056387975 16.76127344923136 30.796736704058596 chr21 48129895 717309830 14.90362341326529 59.345011017434814 chr22 51304566 611537149 11.919741198083617 53.51433901850625 chrMT 16571 112852573 6810.245187375535 1153.1576144630988 chrX 155270560 1493104692 9.616148045064048 43.182205050307125 chrY 59373566 458396604 7.720550320322683 187.45903912893755