BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238045.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 = 1,791,264 number of mapped reads = 1,367,082 (76.32%) number of supplementary alignments = 11,437 (0.64%) number of secondary alignments = 0 number of mapped bases = 86,802,998 bp number of sequenced bases = 86,753,033 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 136,159 duplication rate = 7.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8501 >>>>>>> ACTG content number of A's = 23,212,306 bp (26.76%) number of C's = 15,460,822 bp (17.82%) number of T's = 27,870,508 bp (32.13%) number of G's = 20,059,498 bp (23.12%) number of N's = 149,899 bp (0.17%) GC percentage = 40.94% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 784,605 number of insertions = 6,949 mapped reads with insertion percentage = 0.5% number of deletions = 29,960 mapped reads with deletion percentage = 2.16% homopolymer indels = 45.12% >>>>>>> Coverage mean coverageData = 0.028X std coverageData = 0.4088X There is a 1.91% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% 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 6402086 0.025685336206243595 0.88082510399552 chr2 243199373 3498666 0.014385999259956974 0.3323722660654951 chr3 198022430 5578171 0.0281693896999446 0.25833611288884517 chr4 191154276 5986944 0.03131995854489805 0.2614240837631228 chr5 180915260 10329571 0.05709618414720793 0.3331723123619503 chr6 171115067 6413881 0.037482853570106715 0.45509579749107215 chr7 159138663 5408523 0.03398622872683051 0.3662440489891405 chr8 146364022 5657478 0.03865347455401301 0.354039816875337 chr9 141213431 3054635 0.021631334770132453 0.29090109946550047 chr10 135534747 4278482 0.031567417910921394 0.7137300374673288 chr11 135006516 2769312 0.02051243215549685 0.24616109202197198 chr12 133851895 5036852 0.03763003878279049 0.2742199295658273 chr13 115169878 3615260 0.03139067317584551 0.24595759116519972 chr14 107349540 2893242 0.026951601283060924 0.23368556286999828 chr15 102531392 2954558 0.028816130770954518 0.23669802854191394 chr16 90354753 1326559 0.014681673691255621 0.18567307464707028 chr17 81195210 1593679 0.01962774651361823 0.22488459739578248 chr18 78077248 2529646 0.03239927206450719 0.4760928795165449 chr19 59128983 1531522 0.025901375641789747 0.5665027910261279 chr20 63025520 2020006 0.03205060426316197 0.25397161630408005 chr21 48129895 662490 0.013764625914932912 0.17460011810124904 chr22 51304566 780436 0.015211823446669444 0.16483071873454913 chrMT 16571 29378 1.7728561945567558 1.9347877570173484 chrX 155270560 2173142 0.013995840550842348 0.17611337554577908 chrY 59373566 278479 0.0046902859093893735 0.16792935125784889