BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716683.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,561,473 number of mapped reads = 1,385,578 (88.74%) number of supplementary alignments = 4,949 (0.32%) number of secondary alignments = 0 number of mapped bases = 78,973,640 bp number of sequenced bases = 78,948,969 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,771 duplication rate = 1.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1687 >>>>>>> ACTG content number of A's = 18,458,708 bp (23.38%) number of C's = 16,540,729 bp (20.95%) number of T's = 24,967,305 bp (31.62%) number of G's = 18,981,645 bp (24.04%) number of N's = 582 bp (0%) GC percentage = 44.99% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 415,125 number of insertions = 4,932 mapped reads with insertion percentage = 0.35% number of deletions = 15,165 mapped reads with deletion percentage = 1.09% homopolymer indels = 42.88% >>>>>>> Coverage mean coverageData = 0.0255X std coverageData = 0.2264X There is a 2.33% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 6651664 0.026686649659340266 0.2799812944168922 chr2 243199373 6174373 0.0253881123287271 0.34277466228421644 chr3 198022430 4522680 0.022839230889147254 0.1676212354258397 chr4 191154276 4865297 0.025452200713522097 0.18466932763138036 chr5 180915260 4426564 0.024467609863313908 0.16776636450063778 chr6 171115067 4180961 0.02443362278553764 0.1954582289287467 chr7 159138663 4505766 0.028313458936122894 0.3238506258557163 chr8 146364022 4078288 0.027864006087506943 0.21166444596103406 chr9 141213431 2615110 0.01851884754503274 0.1685712198551111 chr10 135534747 3519746 0.025969325784774587 0.2835251931158635 chr11 135006516 2809464 0.020809840022832676 0.18825917217479932 chr12 133851895 3902755 0.029157263705530654 0.18473060212785564 chr13 115169878 2376215 0.020632261154257713 0.15548137035645782 chr14 107349540 2653721 0.02472037607240795 0.17660977237806197 chr15 102531392 2918298 0.02846248298277273 0.1854420498639954 chr16 90354753 2796156 0.030946418502189918 0.2039755517151156 chr17 81195210 3562565 0.0438765414856369 0.23487628168236324 chr18 78077248 1461860 0.018723252131017734 0.24879081012940443 chr19 59128983 2127832 0.03598627766014511 0.2707708450843026 chr20 63025520 2574291 0.04084521635045613 0.22773498254490748 chr21 48129895 979902 0.020359529145035533 0.1641564650100217 chr22 51304566 751752 0.014652730908979915 0.13253316115550723 chrMT 16571 55770 3.3655180737432864 2.831733271329433 chrX 155270560 4211134 0.027121264971286252 0.18862649962264938 chrY 59373566 251476 0.004235487556870005 0.12220647418127534