BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975232.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 44,231,910 number of mapped reads = 44,144,718 (99.8%) number of supplementary alignments = 169,683 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 22,074,318 number of mapped paired reads (second in pair) = 22,070,400 number of mapped paired reads (both in pair) = 44,082,476 number of mapped paired reads (singletons) = 62,242 number of mapped bases = 4,172,685,235 bp number of sequenced bases = 4,171,233,393 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,068,512 duplication rate = 42.28% >>>>>>> Insert size mean insert size = 218,100.2564 std insert size = 4,643,580.7913 median insert size = 233 >>>>>>> Mapping quality mean mapping quality = 56.0124 >>>>>>> ACTG content number of A's = 1,087,177,811 bp (26.06%) number of C's = 975,474,881 bp (23.39%) number of T's = 1,098,323,298 bp (26.33%) number of G's = 1,010,140,563 bp (24.22%) number of N's = 116,840 bp (0%) GC percentage = 47.6% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 28,217,416 number of insertions = 394,595 mapped reads with insertion percentage = 0.88% number of deletions = 995,654 mapped reads with deletion percentage = 2.22% homopolymer indels = 46.58% >>>>>>> Coverage mean coverageData = 1.3479X std coverageData = 18.8692X There is a 10.03% of reference with a coverageData >= 1X There is a 4.91% of reference with a coverageData >= 2X There is a 3.21% of reference with a coverageData >= 3X There is a 2.59% of reference with a coverageData >= 4X There is a 2.27% of reference with a coverageData >= 5X There is a 2.08% of reference with a coverageData >= 6X There is a 1.93% of reference with a coverageData >= 7X There is a 1.82% of reference with a coverageData >= 8X There is a 1.73% of reference with a coverageData >= 9X There is a 1.64% of reference with a coverageData >= 10X There is a 1.57% of reference with a coverageData >= 11X There is a 1.51% of reference with a coverageData >= 12X There is a 1.45% of reference with a coverageData >= 13X There is a 1.4% of reference with a coverageData >= 14X There is a 1.35% of reference with a coverageData >= 15X There is a 1.3% of reference with a coverageData >= 16X There is a 1.26% of reference with a coverageData >= 17X There is a 1.22% of reference with a coverageData >= 18X There is a 1.18% of reference with a coverageData >= 19X There is a 1.15% of reference with a coverageData >= 20X There is a 1.12% of reference with a coverageData >= 21X There is a 1.09% of reference with a coverageData >= 22X There is a 1.06% of reference with a coverageData >= 23X There is a 1.03% of reference with a coverageData >= 24X There is a 1% of reference with a coverageData >= 25X There is a 0.98% of reference with a coverageData >= 26X There is a 0.96% of reference with a coverageData >= 27X There is a 0.93% of reference with a coverageData >= 28X There is a 0.91% of reference with a coverageData >= 29X There is a 0.89% of reference with a coverageData >= 30X There is a 0.87% of reference with a coverageData >= 31X There is a 0.85% of reference with a coverageData >= 32X There is a 0.83% of reference with a coverageData >= 33X There is a 0.82% of reference with a coverageData >= 34X There is a 0.8% of reference with a coverageData >= 35X There is a 0.78% of reference with a coverageData >= 36X There is a 0.77% of reference with a coverageData >= 37X There is a 0.75% of reference with a coverageData >= 38X There is a 0.74% of reference with a coverageData >= 39X There is a 0.72% of reference with a coverageData >= 40X There is a 0.71% of reference with a coverageData >= 41X There is a 0.69% of reference with a coverageData >= 42X There is a 0.68% of reference with a coverageData >= 43X There is a 0.67% of reference with a coverageData >= 44X There is a 0.66% of reference with a coverageData >= 45X There is a 0.65% of reference with a coverageData >= 46X There is a 0.63% of reference with a coverageData >= 47X There is a 0.62% of reference with a coverageData >= 48X There is a 0.61% of reference with a coverageData >= 49X There is a 0.6% of reference with a coverageData >= 50X There is a 0.59% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 411352313 1.6503562211786826 20.013251191054692 chr2 243199373 340598822 1.4004921879465537 17.741527499172687 chr3 198022430 225054758 1.1365114446883617 15.645822906434377 chr4 191154276 112969884 0.5909880038466939 9.316174570140921 chr5 180915260 175356706 0.969275372348358 14.60887714047799 chr6 171115067 222946423 1.3029035193025988 18.362085769361283 chr7 159138663 178509578 1.1217234997129515 16.853337524821768 chr8 146364022 144567266 0.9877240596736266 14.880847414177957 chr9 141213431 182569312 1.2928608186001798 17.557397946695914 chr10 135534747 166144876 1.2258470958742411 17.020182967312483 chr11 135006516 346442166 2.5661144088778647 28.551260430684675 chr12 133851895 257363937 1.9227515381833034 24.521668420640292 chr13 115169878 59531025 0.5168975259312162 9.42445904904069 chr14 107349540 159964648 1.4901288631511602 19.43441668014623 chr15 102531392 122085448 1.1907128696740994 14.751592924054654 chr16 90354753 116578318 1.2902289489961862 15.927918890524975 chr17 81195210 268605598 3.30814586229902 33.377893367275036 chr18 78077248 61839459 0.7920291837130325 13.358498799203161 chr19 59128983 176876559 2.9913681924818496 31.90231389751686 chr20 63025520 250253648 3.970671689817077 42.68958779685869 chr21 48129895 29160466 0.6058701353909042 9.917838524366063 chr22 51304566 79319534 1.5460521389070907 19.986519977028244 chrMT 16571 101251 6.110132158590308 9.266731768868047 chrX 155270560 77535891 0.49935989797422 8.206532413787585 chrY 59373566 6957349 0.11717923427405388 3.437948428188521