BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004158.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 = 2,023,085 number of mapped reads = 1,790,782 (88.52%) number of supplementary alignments = 17,741 (0.88%) number of secondary alignments = 0 number of mapped bases = 117,943,483 bp number of sequenced bases = 117,863,267 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 79,050 duplication rate = 3.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4177 >>>>>>> ACTG content number of A's = 33,383,065 bp (28.32%) number of C's = 21,353,273 bp (18.12%) number of T's = 37,786,653 bp (32.06%) number of G's = 25,331,242 bp (21.49%) number of N's = 9,034 bp (0.01%) GC percentage = 39.61% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 1,136,451 number of insertions = 9,043 mapped reads with insertion percentage = 0.5% number of deletions = 46,688 mapped reads with deletion percentage = 2.57% homopolymer indels = 43.69% >>>>>>> Coverage mean coverageData = 0.0381X std coverageData = 0.3529X There is a 3.19% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 8821587 0.03539243739737764 0.679075652724088 chr2 243199373 9154270 0.037641009872175946 0.3130292311829848 chr3 198022430 6609247 0.03337625439703977 0.2098025805037707 chr4 191154276 7951191 0.04159567427097472 0.2555366917605686 chr5 180915260 8414323 0.04650974716007925 0.25057576651688357 chr6 171115067 6957384 0.040659096372851845 0.23952266414921478 chr7 159138663 7789101 0.04894537162223111 0.5450650734423835 chr8 146364022 8771597 0.059930007935966666 0.5016117011366957 chr9 141213431 4195676 0.029711593084938218 0.28456095747941046 chr10 135534747 8132449 0.0600026869862383 0.3997952583811198 chr11 135006516 5909781 0.043774042728426533 0.2955500120257307 chr12 133851895 4626378 0.03456341055163993 0.21812382187204277 chr13 115169878 4660299 0.040464564875201135 0.22998087370995732 chr14 107349540 3029810 0.028223781862502625 0.20922549426854561 chr15 102531392 5439790 0.053054873184595015 0.2641351130133348 chr16 90354753 2296172 0.02541285238198814 0.21568629035628104 chr17 81195210 1957564 0.024109353248793864 0.18911300461779096 chr18 78077248 3340323 0.04278228402722391 0.488659942091942 chr19 59128983 1606600 0.027171108287115307 0.4313752601907096 chr20 63025520 1944524 0.0308529624190328 0.2089453741166516 chr21 48129895 2098741 0.043605767267931916 0.26359982944785265 chr22 51304566 869575 0.01694927114284526 0.146171856778987 chrMT 16571 53027 3.1999879307223464 2.682420517967228 chrX 155270560 3027152 0.019495981723773006 0.18232794477781156 chrY 59373566 286922 0.004832487238512842 0.14508002022144345