BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231738.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 = 841,386 number of mapped reads = 553,017 (65.73%) number of supplementary alignments = 3,065 (0.36%) number of secondary alignments = 0 number of mapped bases = 35,687,745 bp number of sequenced bases = 35,667,646 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,943 duplication rate = 2.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8141 >>>>>>> ACTG content number of A's = 10,104,160 bp (28.33%) number of C's = 6,025,601 bp (16.89%) number of T's = 11,761,110 bp (32.97%) number of G's = 7,775,292 bp (21.8%) number of N's = 1,483 bp (0%) GC percentage = 38.69% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 313,457 number of insertions = 2,952 mapped reads with insertion percentage = 0.53% number of deletions = 11,518 mapped reads with deletion percentage = 2.05% homopolymer indels = 45.01% >>>>>>> Coverage mean coverageData = 0.0115X std coverageData = 0.1477X There is a 1.03% of reference with a coverageData >= 1X There is a 0.09% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 2266909 0.009094898102580856 0.19705984978044297 chr2 243199373 1975700 0.00812378739150779 0.11982547093276986 chr3 198022430 4508544 0.0227678450365446 0.1653245531374915 chr4 191154276 846862 0.004430254021625966 0.07610884762837941 chr5 180915260 1141112 0.006307439184511024 0.08610991723437399 chr6 171115067 3250533 0.018996182259040928 0.16697233806501602 chr7 159138663 2426694 0.015248927911377514 0.18076674836978865 chr8 146364022 2498966 0.017073635760023048 0.2961616679712114 chr9 141213431 1452134 0.01028325697999647 0.11843873981348362 chr10 135534747 1778912 0.013125136095174177 0.1417117496247456 chr11 135006516 1384218 0.01025297178989494 0.12528985871940673 chr12 133851895 1898779 0.014185671409433538 0.1304061156793583 chr13 115169878 1920173 0.01667252786357905 0.14159377774383886 chr14 107349540 1584639 0.01476148849822738 0.13486967724899065 chr15 102531392 495118 0.00482894058436269 0.07647929067873639 chr16 90354753 1272532 0.014083730603524532 0.13166371718993972 chr17 81195210 967444 0.01191503784521279 0.12362222693107944 chr18 78077248 619418 0.007933399496867513 0.16883422803884512 chr19 59128983 787657 0.013320996912799938 0.14998057072091603 chr20 63025520 748158 0.01187071522773632 0.11891893042621134 chr21 48129895 420601 0.008738872170820236 0.10325159210725644 chr22 51304566 281673 0.0054902130933141505 0.07993729107105914 chrMT 16571 32221 1.9444209764045621 1.8828963527793885 chrX 155270560 1048590 0.006753308547351153 0.0919849653095848 chrY 59373566 80158 0.001350062079815115 0.04618647093468974