BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716846.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 = 3,379,572 number of mapped reads = 3,172,875 (93.88%) number of supplementary alignments = 56,962 (1.69%) number of secondary alignments = 0 number of mapped bases = 247,888,254 bp number of sequenced bases = 247,780,122 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 186,626 duplication rate = 4.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6605 >>>>>>> ACTG content number of A's = 63,867,472 bp (25.78%) number of C's = 48,617,664 bp (19.62%) number of T's = 76,047,444 bp (30.69%) number of G's = 59,229,856 bp (23.9%) number of N's = 17,686 bp (0.01%) GC percentage = 43.53% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 1,599,496 number of insertions = 21,946 mapped reads with insertion percentage = 0.68% number of deletions = 57,424 mapped reads with deletion percentage = 1.78% homopolymer indels = 41.7% >>>>>>> Coverage mean coverageData = 0.0801X std coverageData = 0.6176X There is a 6.31% of reference with a coverageData >= 1X There is a 1.15% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.08% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 20047091 0.08042945257095267 1.097010050858573 chr2 243199373 20911557 0.08598524223991318 0.7896979181548933 chr3 198022430 16036453 0.08098301288394451 0.3443935053827222 chr4 191154276 15609916 0.08166134876313204 0.4689517198716202 chr5 180915260 15148955 0.08373508680251737 0.35777668147812014 chr6 171115067 14395877 0.08412980371857026 0.4140011114260202 chr7 159138663 13654075 0.08579985996237759 0.8683607194767529 chr8 146364022 12716593 0.08688332573970944 0.7942825640181356 chr9 141213431 10355409 0.07333161531922555 0.5608850775949556 chr10 135534747 11605244 0.08562559975856228 0.6160607313115563 chr11 135006516 11507353 0.0852355378165599 0.62026401707392 chr12 133851895 11316908 0.08454798492019855 0.3567748746540209 chr13 115169878 7930875 0.06886240688732864 0.3184618360665559 chr14 107349540 7491639 0.06978734142689387 0.35885298952192324 chr15 102531392 7216142 0.07037983059861315 0.32293709056644 chr16 90354753 7251373 0.08025447205859773 0.3822257523434265 chr17 81195210 6720423 0.08276871258784847 0.43190064010286083 chr18 78077248 6761916 0.08660546027441951 0.9607354814726389 chr19 59128983 4893665 0.08276254303240764 0.7703395394545527 chr20 63025520 5300129 0.08409496661035086 0.37628442500061643 chr21 48129895 3366822 0.06995282246096735 0.3998711819180895 chr22 51304566 2898771 0.05650122837020003 0.2940053329363075 chrMT 16571 22482 1.3567075010560619 1.6407724362361418 chrX 155270560 14021413 0.09030310060065476 0.4579367486328162 chrY 59373566 707173 0.011910569764329129 0.37144979788565