BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068068.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 = 4,672,675 number of mapped reads = 4,488,725 (96.06%) number of supplementary alignments = 43,773 (0.94%) number of secondary alignments = 0 number of mapped bases = 296,636,914 bp number of sequenced bases = 296,540,467 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,392,390 duplication rate = 16.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1819 >>>>>>> ACTG content number of A's = 79,459,614 bp (26.8%) number of C's = 53,788,189 bp (18.14%) number of T's = 96,006,073 bp (32.38%) number of G's = 67,251,528 bp (22.68%) number of N's = 35,063 bp (0.01%) GC percentage = 40.82% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 1,402,890 number of insertions = 20,784 mapped reads with insertion percentage = 0.46% number of deletions = 54,128 mapped reads with deletion percentage = 1.19% homopolymer indels = 45.98% >>>>>>> Coverage mean coverageData = 0.0958X std coverageData = 1.1084X There is a 3% of reference with a coverageData >= 1X There is a 1.93% of reference with a coverageData >= 2X There is a 1.36% of reference with a coverageData >= 3X There is a 0.96% of reference with a coverageData >= 4X There is a 0.67% of reference with a coverageData >= 5X There is a 0.47% of reference with a coverageData >= 6X There is a 0.32% of reference with a coverageData >= 7X There is a 0.22% of reference with a coverageData >= 8X There is a 0.15% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% 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 34151682 0.13701743996858487 1.8102771973639658 chr2 243199373 30223757 0.12427563700996877 1.1726014131418385 chr3 198022430 17999307 0.09089529403310524 0.7139423552571373 chr4 191154276 16062208 0.08402745853302282 0.7499400767948405 chr5 180915260 14313807 0.07911884823867263 0.6490840980656787 chr6 171115067 18043246 0.10544510379088944 0.8058965355004138 chr7 159138663 21791197 0.13693213571864682 1.572604861949732 chr8 146364022 14328417 0.09789575883614349 2.463178302833308 chr9 141213431 8992358 0.06367919776696028 0.7309102132420652 chr10 135534747 13335737 0.09839349167044227 0.933429104542762 chr11 135006516 16344160 0.12106200859223713 0.861115966232399 chr12 133851895 12799109 0.09562142545684542 0.7346939003340619 chr13 115169878 5880078 0.051055693572932326 0.546751911866301 chr14 107349540 5673309 0.052848936287943106 0.5711961588176608 chr15 102531392 5643783 0.05504443946298905 0.5368272849171877 chr16 90354753 6754683 0.07475736223859746 0.6646725926887262 chr17 81195210 7807272 0.09615434210958997 0.7376112814893924 chr18 78077248 8253965 0.10571536793919786 1.33789360873958 chr19 59128983 5897573 0.09974081576880833 1.158567794488637 chr20 63025520 3994124 0.0633731225065656 0.6435874333970282 chr21 48129895 6180804 0.12841922883895757 0.8692056862459369 chr22 51304566 2661113 0.05186893112008783 0.5136864930171204 chrMT 16571 239321 14.442157986844487 14.274413680559162 chrX 155270560 18475136 0.11898672871405887 0.8439573251521546 chrY 59373566 790768 0.013318519558013409 0.42497112052063934