BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6003986.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,069,043 number of mapped reads = 1,544,337 (74.64%) number of supplementary alignments = 10,597 (0.51%) number of secondary alignments = 0 number of mapped bases = 98,376,577 bp number of sequenced bases = 98,329,342 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 261,198 duplication rate = 12.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6663 >>>>>>> ACTG content number of A's = 26,023,459 bp (26.47%) number of C's = 18,675,354 bp (18.99%) number of T's = 30,692,477 bp (31.21%) number of G's = 22,918,749 bp (23.31%) number of N's = 19,303 bp (0.02%) GC percentage = 42.3% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 948,289 number of insertions = 7,584 mapped reads with insertion percentage = 0.49% number of deletions = 28,617 mapped reads with deletion percentage = 1.83% homopolymer indels = 47.65% >>>>>>> Coverage mean coverageData = 0.0318X std coverageData = 0.378X There is a 1.51% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.4% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 9853087 0.039530842332384804 0.48784701260508834 chr2 243199373 9148802 0.03761852626157881 0.5112479081715519 chr3 198022430 6407862 0.03235927364389984 0.32853195414075353 chr4 191154276 5957104 0.03116385426816191 0.31689674226745923 chr5 180915260 5655957 0.031263017834979756 0.3207526285159193 chr6 171115067 6333354 0.03701225211220003 0.3803947288824453 chr7 159138663 5192517 0.032628884157459584 0.44329145799112496 chr8 146364022 5696668 0.03892123161250652 0.40605886275551584 chr9 141213431 3746969 0.0265340837161587 0.3365912226858395 chr10 135534747 4200015 0.030988474121695156 0.3507977081473899 chr11 135006516 3914902 0.028997874443334275 0.3713005649312853 chr12 133851895 4016072 0.030003848656756035 0.3131694702877043 chr13 115169878 2159849 0.01875359284482354 0.24293371164622038 chr14 107349540 2523453 0.023506882283799258 0.2997595714014703 chr15 102531392 2577805 0.025141617115663463 0.2851479356930368 chr16 90354753 3170605 0.03509062771717167 0.3496116831053474 chr17 81195210 2598298 0.03200063156434967 0.33590674712344987 chr18 78077248 2641701 0.03383445328400919 0.5300033200632839 chr19 59128983 1903143 0.03218629686223421 0.41485287932043685 chr20 63025520 2549431 0.040450772956732446 0.3736902197470987 chr21 48129895 1569875 0.032617461558974936 0.3431399584397164 chr22 51304566 1195517 0.023302350905765386 0.28059865155458147 chrMT 16571 96505 5.823728199867238 7.047029363381554 chrX 155270560 5036117 0.032434461497401694 0.3387281900241271 chrY 59373566 230969 0.0038900981625392015 0.10383805540270045