BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174022.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 2,862,550 number of mapped reads = 2,782,375 (97.2%) number of supplementary alignments = 285,511 (9.97%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,394,471 number of mapped paired reads (second in pair) = 1,387,904 number of mapped paired reads (both in pair) = 2,729,346 number of mapped paired reads (singletons) = 53,029 number of mapped bases = 326,719,824 bp number of sequenced bases = 326,538,401 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,141,868 duplication rate = 64.36% >>>>>>> Insert size mean insert size = 866,512.9707 std insert size = 9,001,937.8428 median insert size = 194 >>>>>>> Mapping quality mean mapping quality = 52.6673 >>>>>>> ACTG content number of A's = 98,412,918 bp (30.14%) number of C's = 63,838,427 bp (19.55%) number of T's = 98,092,590 bp (30.04%) number of G's = 66,190,231 bp (20.27%) number of N's = 4,235 bp (0%) GC percentage = 39.82% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 3,369,705 number of insertions = 33,067 mapped reads with insertion percentage = 1.15% number of deletions = 72,747 mapped reads with deletion percentage = 2.55% homopolymer indels = 43.25% >>>>>>> Coverage mean coverageData = 0.1055X std coverageData = 1.7135X There is a 2.28% of reference with a coverageData >= 1X There is a 1.78% of reference with a coverageData >= 2X There is a 1.36% of reference with a coverageData >= 3X There is a 1.11% of reference with a coverageData >= 4X There is a 0.83% of reference with a coverageData >= 5X There is a 0.67% of reference with a coverageData >= 6X There is a 0.49% of reference with a coverageData >= 7X There is a 0.4% of reference with a coverageData >= 8X There is a 0.29% of reference with a coverageData >= 9X There is a 0.24% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.15% of reference with a coverageData >= 12X There is a 0.11% of reference with a coverageData >= 13X There is a 0.1% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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 35889388 0.14398916181637117 1.4947319487691921 chr2 243199373 32233147 0.1325379527191462 4.7787975154361195 chr3 198022430 25422641 0.12838263321988322 1.0326006836976205 chr4 191154276 19048880 0.09965186444482152 1.0103092937191847 chr5 180915260 21734040 0.12013381292434923 0.9916828026736612 chr6 171115067 17733741 0.10363635015261397 0.9385626715200107 chr7 159138663 20541428 0.12907880217643905 1.4345621947350868 chr8 146364022 13126600 0.08968460842105036 0.97044368156392 chr9 141213431 13145014 0.09308614560891167 0.9573454668515481 chr10 135534747 12767422 0.09420036029579927 1.7703892321213917 chr11 135006516 15099870 0.11184549047988172 0.974448617338321 chr12 133851895 11500176 0.08591716986898093 0.8327661407179803 chr13 115169878 10516207 0.09131039454604614 0.8686485473464501 chr14 107349540 7598885 0.0707863769141442 0.7596465613522809 chr15 102531392 10324108 0.10069216655129387 0.8886456242693191 chr16 90354753 12990011 0.14376677007793934 1.3802699244386376 chr17 81195210 7456837 0.09183838554023076 0.9035846558942193 chr18 78077248 5228042 0.06695986518377287 1.1867161146693912 chr19 59128983 5855920 0.09903637273788389 1.4066444176107107 chr20 63025520 8693497 0.1379361407886837 1.053785416147234 chr21 48129895 4800894 0.09974869049683155 0.9106432916639375 chr22 51304566 2720159 0.053019822836041536 0.6279295597802175 chrMT 16571 863428 52.1047613300344 45.33241820621193 chrX 155270560 10989844 0.07077867175850978 0.7606385521264433 chrY 59373566 439645 0.007404726204250559 0.344625346339204