BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240068.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 = 1,057,481 number of mapped reads = 718,647 (67.96%) number of supplementary alignments = 6,105 (0.58%) number of secondary alignments = 0 number of mapped bases = 45,562,242 bp number of sequenced bases = 45,538,968 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,863 duplication rate = 9.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46 >>>>>>> ACTG content number of A's = 12,863,557 bp (28.25%) number of C's = 8,254,271 bp (18.13%) number of T's = 14,659,064 bp (32.19%) number of G's = 9,733,484 bp (21.37%) number of N's = 28,592 bp (0.06%) GC percentage = 39.5% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 436,616 number of insertions = 3,358 mapped reads with insertion percentage = 0.46% number of deletions = 13,525 mapped reads with deletion percentage = 1.86% homopolymer indels = 48.23% >>>>>>> Coverage mean coverageData = 0.0147X std coverageData = 0.2305X There is a 0.86% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% 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 3303125 0.013252223752734401 0.2919645836471525 chr2 243199373 3614439 0.014862040783304158 0.23363432059486403 chr3 198022430 2768772 0.013982113036386837 0.18785131836127678 chr4 191154276 2543375 0.0133053523741211 0.19202607886802894 chr5 180915260 2744468 0.015169908829139123 0.19754178289418522 chr6 171115067 2820912 0.016485468225892697 0.22328053485244712 chr7 159138663 2324254 0.014605212562329998 0.24825671679145841 chr8 146364022 2270927 0.015515609430301116 0.3256570308734998 chr9 141213431 1839034 0.013023081352651221 0.2128282153321542 chr10 135534747 2506249 0.018491560691812854 0.23813505779420674 chr11 135006516 2026317 0.015009031119653514 0.22216713589045578 chr12 133851895 2571457 0.019211211017968778 0.24031728604671548 chr13 115169878 1568934 0.013622780776063687 0.19681459778545182 chr14 107349540 1783775 0.016616512748913504 0.22710099756771907 chr15 102531392 1810697 0.017659927995515756 0.24332060915945444 chr16 90354753 1258480 0.013928210284632177 0.19470861124838884 chr17 81195210 1069540 0.013172451921732822 0.1932908824707979 chr18 78077248 1131424 0.014491084521831506 0.30603431024504457 chr19 59128983 660387 0.011168583772191718 0.21247076193345538 chr20 63025520 1148329 0.01822006387253925 0.2322936260032631 chr21 48129895 627363 0.013034788461516485 0.19038694428506972 chr22 51304566 481297 0.009381172818029491 0.15359992499955913 chrMT 16571 24451 1.4755295395570576 2.0812401326857204 chrX 155270560 2534072 0.016320363628494674 0.21431788793542908 chrY 59373566 130164 0.002192288736708184 0.08007390257230654