BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004126.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 = 2,692,452 number of mapped reads = 2,150,657 (79.88%) number of supplementary alignments = 13,873 (0.52%) number of secondary alignments = 0 number of mapped bases = 142,364,542 bp number of sequenced bases = 142,296,134 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 98,839 duplication rate = 3.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.2506 >>>>>>> ACTG content number of A's = 38,729,812 bp (27.22%) number of C's = 25,863,848 bp (18.18%) number of T's = 45,191,334 bp (31.76%) number of G's = 32,496,232 bp (22.84%) number of N's = 14,908 bp (0.01%) GC percentage = 41.01% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 1,456,925 number of insertions = 13,506 mapped reads with insertion percentage = 0.62% number of deletions = 40,524 mapped reads with deletion percentage = 1.86% homopolymer indels = 46.69% >>>>>>> Coverage mean coverageData = 0.046X std coverageData = 0.5955X There is a 3.95% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.07% 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 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 15135086 0.06072236024639634 1.4846362850479582 chr2 243199373 8643656 0.03554144031448634 0.6604789303405038 chr3 198022430 5706748 0.0288186949326902 0.19822103625818024 chr4 191154276 4743272 0.02481384198802856 0.1874835427579217 chr5 180915260 11553693 0.06386245693149378 0.28624970547170275 chr6 171115067 8962121 0.05237482097353823 0.34210724520249347 chr7 159138663 10456029 0.06570388868982768 0.8701561475751508 chr8 146364022 6547772 0.04473621256458776 0.45920497175344094 chr9 141213431 3893408 0.02757108847528816 0.3846549652852058 chr10 135534747 9012854 0.06649847511059286 0.510043261627493 chr11 135006516 5280478 0.03911276400910901 0.3101644162524201 chr12 133851895 6172455 0.046114065101581114 0.24564299936179518 chr13 115169878 3955599 0.034345777461012854 0.20360281284936532 chr14 107349540 4410693 0.041087209130099674 0.24399998139677864 chr15 102531392 3997646 0.038989483337942006 0.2329322540300888 chr16 90354753 4334928 0.047976756684842026 0.2834456386152188 chr17 81195210 2928172 0.03606335890996525 0.23507410441046855 chr18 78077248 4813487 0.0616503158512964 0.7665715632115825 chr19 59128983 2779411 0.047005898951449916 0.9486751141049875 chr20 63025520 5364073 0.08510953975468985 0.3646544898412975 chr21 48129895 2607349 0.054173170334155106 0.2678604499095006 chr22 51304566 839465 0.016362383808100043 0.1400890588507764 chrMT 16571 36534 2.204694949007302 2.111340222151434 chrX 155270560 9810599 0.06318389654806424 0.3767006864567388 chrY 59373566 379014 0.006383547856970559 0.12557930594163974