BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008757.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 = 2,141,052 number of mapped reads = 1,957,527 (91.43%) number of supplementary alignments = 7,683 (0.36%) number of secondary alignments = 0 number of mapped bases = 129,386,411 bp number of sequenced bases = 129,321,504 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 76,480 duplication rate = 2.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5414 >>>>>>> ACTG content number of A's = 34,202,997 bp (26.45%) number of C's = 24,810,882 bp (19.19%) number of T's = 39,657,824 bp (30.67%) number of G's = 30,450,105 bp (23.55%) number of N's = 199,696 bp (0.15%) GC percentage = 42.73% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,112,500 number of insertions = 9,887 mapped reads with insertion percentage = 0.5% number of deletions = 36,404 mapped reads with deletion percentage = 1.84% homopolymer indels = 44.67% >>>>>>> Coverage mean coverageData = 0.0418X std coverageData = 0.4712X There is a 3.59% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.06% 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 11861195 0.047587424065033725 0.875927478846797 chr2 243199373 13056411 0.053686038902740096 0.5854555468673179 chr3 198022430 8580531 0.043331106481220336 0.3206912611656866 chr4 191154276 5229350 0.027356699046585806 0.218986771045765 chr5 180915260 5491365 0.03035324383360475 0.1945176457899962 chr6 171115067 5786535 0.03381663053669026 0.24102704808748243 chr7 159138663 7091281 0.044560390707819385 0.6056562363156589 chr8 146364022 10480804 0.07160778896879454 0.4384322467074512 chr9 141213431 3232057 0.02288774500493512 0.3364626891205017 chr10 135534747 7104198 0.0524160641993894 0.9536465912353483 chr11 135006516 6066691 0.04493628292726256 0.3794280640567472 chr12 133851895 5837793 0.043613824070253174 0.23423101674911953 chr13 115169878 3560466 0.030914906413289766 0.1942546094938321 chr14 107349540 4765212 0.044389682526818464 0.2455637994006827 chr15 102531392 2933199 0.028607814082929842 0.18763185496948684 chr16 90354753 3604779 0.03989584255739153 0.3697206470570993 chr17 81195210 4364501 0.05375318322349311 0.35238362081222735 chr18 78077248 2483633 0.031809945452995474 0.6134855683998065 chr19 59128983 3503468 0.05925128122024355 0.5863773083848512 chr20 63025520 3324643 0.052750742873680374 0.2674665819724278 chr21 48129895 1424411 0.02959514040078417 0.22010909348632376 chr22 51304566 1787770 0.034846216221768644 0.20905577425091443 chrMT 16571 164434 9.922998008569188 5.448618643206776 chrX 155270560 7199215 0.04636561496268191 0.27691692589813466 chrY 59373566 452469 0.00762071457860557 0.25159703323706545