BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777261.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 82,566,514 number of mapped reads = 82,373,923 (99.77%) number of supplementary alignments = 2,429,965 (2.94%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 41,190,527 number of mapped paired reads (second in pair) = 41,183,396 number of mapped paired reads (both in pair) = 82,315,312 number of mapped paired reads (singletons) = 58,611 number of mapped bases = 8,269,027,448 bp number of sequenced bases = 8,267,781,995 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,135,968 duplication rate = 43.51% >>>>>>> Insert size mean insert size = 282,107.1536 std insert size = 5,239,592.7588 median insert size = 248 >>>>>>> Mapping quality mean mapping quality = 54.6964 >>>>>>> ACTG content number of A's = 2,274,234,720 bp (27.51%) number of C's = 1,842,661,759 bp (22.29%) number of T's = 2,255,666,343 bp (27.28%) number of G's = 1,856,126,318 bp (22.45%) number of N's = 39,092,855 bp (0.47%) GC percentage = 44.74% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 58,058,127 number of insertions = 1,600,775 mapped reads with insertion percentage = 1.91% number of deletions = 581,053 mapped reads with deletion percentage = 0.7% homopolymer indels = 51.07% >>>>>>> Coverage mean coverageData = 2.6711X std coverageData = 24.3865X There is a 24.26% of reference with a coverageData >= 1X There is a 13.52% of reference with a coverageData >= 2X There is a 8.52% of reference with a coverageData >= 3X There is a 6.22% of reference with a coverageData >= 4X There is a 4.94% of reference with a coverageData >= 5X There is a 4.2% of reference with a coverageData >= 6X There is a 3.71% of reference with a coverageData >= 7X There is a 3.37% of reference with a coverageData >= 8X There is a 3.11% of reference with a coverageData >= 9X There is a 2.92% of reference with a coverageData >= 10X There is a 2.76% of reference with a coverageData >= 11X There is a 2.62% of reference with a coverageData >= 12X There is a 2.51% of reference with a coverageData >= 13X There is a 2.41% of reference with a coverageData >= 14X There is a 2.33% of reference with a coverageData >= 15X There is a 2.25% of reference with a coverageData >= 16X There is a 2.18% of reference with a coverageData >= 17X There is a 2.11% of reference with a coverageData >= 18X There is a 2.05% of reference with a coverageData >= 19X There is a 2% of reference with a coverageData >= 20X There is a 1.94% of reference with a coverageData >= 21X There is a 1.89% of reference with a coverageData >= 22X There is a 1.85% of reference with a coverageData >= 23X There is a 1.8% of reference with a coverageData >= 24X There is a 1.76% of reference with a coverageData >= 25X There is a 1.72% of reference with a coverageData >= 26X There is a 1.69% of reference with a coverageData >= 27X There is a 1.65% of reference with a coverageData >= 28X There is a 1.62% of reference with a coverageData >= 29X There is a 1.58% of reference with a coverageData >= 30X There is a 1.55% of reference with a coverageData >= 31X There is a 1.52% of reference with a coverageData >= 32X There is a 1.49% of reference with a coverageData >= 33X There is a 1.47% of reference with a coverageData >= 34X There is a 1.44% of reference with a coverageData >= 35X There is a 1.41% of reference with a coverageData >= 36X There is a 1.39% of reference with a coverageData >= 37X There is a 1.36% of reference with a coverageData >= 38X There is a 1.34% of reference with a coverageData >= 39X There is a 1.32% of reference with a coverageData >= 40X There is a 1.3% of reference with a coverageData >= 41X There is a 1.27% of reference with a coverageData >= 42X There is a 1.25% of reference with a coverageData >= 43X There is a 1.23% of reference with a coverageData >= 44X There is a 1.21% of reference with a coverageData >= 45X There is a 1.2% of reference with a coverageData >= 46X There is a 1.18% of reference with a coverageData >= 47X There is a 1.16% of reference with a coverageData >= 48X There is a 1.14% of reference with a coverageData >= 49X There is a 1.13% of reference with a coverageData >= 50X There is a 1.11% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 853522218 3.424353426184643 27.73779425979145 chr2 243199373 717485752 2.950195730973369 25.027156734755664 chr3 198022430 486362835 2.4560997206225577 23.189795857129422 chr4 191154276 359947061 1.8830186199967611 19.15732148406847 chr5 180915260 421930346 2.332198765322505 22.100508779502572 chr6 171115067 389089568 2.2738475040307233 22.353929124786735 chr7 159138663 539188395 3.3881671797129527 29.35851634680871 chr8 146364022 268223091 1.8325752964072004 19.63414169310516 chr9 141213431 279017943 1.9758598103887157 18.953980751659905 chr10 135534747 351656493 2.5945855272080154 23.44948502341352 chr11 135006516 575379090 4.261861627478781 34.466612202264706 chr12 133851895 469612381 3.508447758621572 27.779500252600034 chr13 115169878 232966033 2.022803505965336 21.922384652202272 chr14 107349540 186583513 1.7380932698919809 18.650747339447562 chr15 102531392 381244983 3.7183244620340274 30.50678576132522 chr16 90354753 240094375 2.6572412300214023 21.096116675812805 chr17 81195210 371279251 4.572674311698929 32.18838757518459 chr18 78077248 127802983 1.636878684556095 17.303512765218503 chr19 59128983 422500466 7.145403904545424 42.76867004723381 chr20 63025520 225723316 3.581459002638931 27.913476834707243 chr21 48129895 54689253 1.1362844859728034 14.212754904172195 chr22 51304566 90614373 1.7662048442238065 16.065000848794877 chrMT 16571 2573029 155.27300706052742 52.38056190347387 chrX 155270560 219155309 1.41144147995602 16.743272128754462 chrY 59373566 2385391 0.04017597662906082 1.6408459123933201