BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716725.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 = 1,880,910 number of mapped reads = 1,694,887 (90.11%) number of supplementary alignments = 8,288 (0.44%) number of secondary alignments = 0 number of mapped bases = 97,364,929 bp number of sequenced bases = 97,336,212 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,244 duplication rate = 2.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9542 >>>>>>> ACTG content number of A's = 23,888,836 bp (24.54%) number of C's = 20,079,870 bp (20.63%) number of T's = 30,856,028 bp (31.7%) number of G's = 22,510,371 bp (23.13%) number of N's = 1,107 bp (0%) GC percentage = 43.76% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 497,958 number of insertions = 6,362 mapped reads with insertion percentage = 0.37% number of deletions = 18,369 mapped reads with deletion percentage = 1.08% homopolymer indels = 41.67% >>>>>>> Coverage mean coverageData = 0.0315X std coverageData = 0.3121X There is a 2.81% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 7993414 0.03206978569573955 0.43213442475200875 chr2 243199373 9421372 0.038739293953689594 0.3952311643376793 chr3 198022430 7107453 0.03589216130718121 0.22065899077640802 chr4 191154276 5276721 0.027604514585904426 0.1971206828268079 chr5 180915260 4800961 0.026537070449446885 0.17853477293964465 chr6 171115067 5345942 0.031241795908013174 0.21104401334034903 chr7 159138663 5995594 0.03767528196463483 0.7133783905533243 chr8 146364022 7957667 0.05436901016562663 0.33195894092625017 chr9 141213431 4103731 0.02906048646321751 0.21681892500447275 chr10 135534747 4577343 0.03377246869395049 0.3975220977836875 chr11 135006516 3498393 0.025912771499117866 0.2148126445962566 chr12 133851895 4537575 0.03389996831946234 0.22141551308302931 chr13 115169878 2510748 0.021800387771531718 0.16170719943238065 chr14 107349540 2398520 0.022343085960126144 0.1692191613504998 chr15 102531392 2287547 0.022310698756533024 0.1649281959792165 chr16 90354753 2924087 0.03236229310482427 0.20784252978584028 chr17 81195210 4059497 0.04999675473466969 0.2572148792061149 chr18 78077248 2173898 0.02784291270102143 0.3048373212734619 chr19 59128983 1960552 0.033157208200249276 0.3734547857158232 chr20 63025520 2186053 0.0346852037079583 0.2138555765763914 chr21 48129895 969776 0.020149140154990988 0.15863444578074984 chr22 51304566 1520352 0.029633853641798664 0.18883587723335332 chrMT 16571 185467 11.192263593023958 7.010423474695606 chrX 155270560 3366005 0.02167832073253294 0.18670593521936157 chrY 59373566 206261 0.00347395337514341 0.08913569705377779