BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8617553.sorted.bam outfile = /mainsd2/zhouyj/SRP186739/SRP186739.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 = 57,483,258 number of mapped reads = 56,499,645 (98.29%) number of supplementary alignments = 1,815,416 (3.16%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 28,523,677 number of mapped paired reads (second in pair) = 27,975,968 number of mapped paired reads (both in pair) = 55,837,688 number of mapped paired reads (singletons) = 661,957 number of mapped bases = 7,537,417,521 bp number of sequenced bases = 7,531,978,627 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,771,239 duplication rate = 24.9% >>>>>>> Insert size mean insert size = 233,672.6749 std insert size = 4,689,383.9581 median insert size = 259 >>>>>>> Mapping quality mean mapping quality = 53.3618 >>>>>>> ACTG content number of A's = 2,170,386,634 bp (28.82%) number of C's = 1,438,201,718 bp (19.09%) number of T's = 2,248,110,421 bp (29.85%) number of G's = 1,674,984,920 bp (22.24%) number of N's = 294,934 bp (0%) GC percentage = 41.33% >>>>>>> Mismatches and indels general error rate = 0.0116 number of mismatches = 84,176,273 number of insertions = 1,280,566 mapped reads with insertion percentage = 2.13% number of deletions = 2,769,403 mapped reads with deletion percentage = 4.71% homopolymer indels = 46.53% >>>>>>> Coverage mean coverageData = 2.4348X std coverageData = 23.7208X There is a 39.09% of reference with a coverageData >= 1X There is a 29.94% of reference with a coverageData >= 2X There is a 23.56% of reference with a coverageData >= 3X There is a 19.2% of reference with a coverageData >= 4X There is a 15.8% of reference with a coverageData >= 5X There is a 13.21% of reference with a coverageData >= 6X There is a 11.13% of reference with a coverageData >= 7X There is a 9.46% of reference with a coverageData >= 8X There is a 8.1% of reference with a coverageData >= 9X There is a 6.97% of reference with a coverageData >= 10X There is a 6.03% of reference with a coverageData >= 11X There is a 5.24% of reference with a coverageData >= 12X There is a 4.57% of reference with a coverageData >= 13X There is a 4% of reference with a coverageData >= 14X There is a 3.52% of reference with a coverageData >= 15X There is a 3.1% of reference with a coverageData >= 16X There is a 2.74% of reference with a coverageData >= 17X There is a 2.44% of reference with a coverageData >= 18X There is a 2.17% of reference with a coverageData >= 19X There is a 1.93% of reference with a coverageData >= 20X There is a 1.73% of reference with a coverageData >= 21X There is a 1.54% of reference with a coverageData >= 22X There is a 1.39% of reference with a coverageData >= 23X There is a 1.25% of reference with a coverageData >= 24X There is a 1.12% of reference with a coverageData >= 25X There is a 1.01% of reference with a coverageData >= 26X There is a 0.92% of reference with a coverageData >= 27X There is a 0.83% of reference with a coverageData >= 28X There is a 0.75% of reference with a coverageData >= 29X There is a 0.69% of reference with a coverageData >= 30X There is a 0.62% of reference with a coverageData >= 31X There is a 0.57% of reference with a coverageData >= 32X There is a 0.52% of reference with a coverageData >= 33X There is a 0.48% of reference with a coverageData >= 34X There is a 0.43% of reference with a coverageData >= 35X There is a 0.4% of reference with a coverageData >= 36X There is a 0.37% of reference with a coverageData >= 37X There is a 0.34% of reference with a coverageData >= 38X There is a 0.31% of reference with a coverageData >= 39X There is a 0.29% of reference with a coverageData >= 40X There is a 0.26% of reference with a coverageData >= 41X There is a 0.25% of reference with a coverageData >= 42X There is a 0.23% of reference with a coverageData >= 43X There is a 0.21% of reference with a coverageData >= 44X There is a 0.2% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 616276582 2.4725177394843882 27.400944523247894 chr2 243199373 675129096 2.776031400377007 27.19142454022176 chr3 198022430 518719868 2.6195005686982027 5.714725567019003 chr4 191154276 473567172 2.4774082061339815 19.7117474815688 chr5 180915260 788457835 4.358161025222527 9.542230242340784 chr6 171115067 442788159 2.5876631833945987 21.152968765810407 chr7 159138663 310564297 1.951532651747866 22.412835084005653 chr8 146364022 376379320 2.571528951288316 9.629976660582642 chr9 141213431 327422328 2.3186344647344486 40.229646145440356 chr10 135534747 329876351 2.433887680477981 54.00462394061334 chr11 135006516 354914563 2.6288698761769393 16.84290041475079 chr12 133851895 330532149 2.469387146143878 10.975166836249125 chr13 115169878 187766180 1.6303410515030674 4.275113377001476 chr14 107349540 225627669 2.101803780435389 5.462287600574855 chr15 102531392 216927490 2.115717789143056 6.675312031306568 chr16 90354753 258473619 2.8606532630331025 42.58246136687379 chr17 81195210 159552930 1.9650534803715638 18.86787743019713 chr18 78077248 214208472 2.743545366762927 34.80659465883973 chr19 59128983 102181453 1.7281111193811671 15.161210855634105 chr20 63025520 164160917 2.604673741684321 8.024446033801848 chr21 48129895 92815439 1.9284363491754968 10.297394904750366 chr22 51304566 41271013 0.8044315782731697 3.6474435903908495 chrMT 16571 2764667 166.8376682155573 82.7488238675705 chrX 155270560 223703589 1.4407340902228987 6.879588538902414 chrY 59373566 103336363 1.7404439376270577 40.94872135574524