BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008770.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 = 5,680,662 number of mapped reads = 4,266,321 (75.1%) number of supplementary alignments = 39,525 (0.7%) number of secondary alignments = 0 number of mapped bases = 276,798,211 bp number of sequenced bases = 276,692,557 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 973,199 duplication rate = 15.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.0891 >>>>>>> ACTG content number of A's = 75,638,836 bp (27.34%) number of C's = 48,636,934 bp (17.58%) number of T's = 90,422,769 bp (32.68%) number of G's = 61,905,290 bp (22.37%) number of N's = 88,728 bp (0.03%) GC percentage = 39.95% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 2,093,847 number of insertions = 19,662 mapped reads with insertion percentage = 0.46% number of deletions = 66,110 mapped reads with deletion percentage = 1.54% homopolymer indels = 48.73% >>>>>>> Coverage mean coverageData = 0.0894X std coverageData = 0.892X There is a 3.08% of reference with a coverageData >= 1X There is a 1.87% of reference with a coverageData >= 2X There is a 1.24% of reference with a coverageData >= 3X There is a 0.82% of reference with a coverageData >= 4X There is a 0.55% of reference with a coverageData >= 5X There is a 0.37% of reference with a coverageData >= 6X There is a 0.25% of reference with a coverageData >= 7X There is a 0.18% of reference with a coverageData >= 8X There is a 0.13% of reference with a coverageData >= 9X There is a 0.09% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 6297700 0.02526653684846787 0.3941879467646226 chr2 243199373 48867556 0.20093619238072624 1.1900024434586542 chr3 198022430 23793689 0.1201565347925485 0.8039310647887264 chr4 191154276 18452833 0.09653371813665314 0.6971319849592419 chr5 180915260 11787161 0.06515293955855354 0.5804120398365538 chr6 171115067 4002128 0.02338851902503711 0.358567075575765 chr7 159138663 14187356 0.08915090608747919 0.7177642127087421 chr8 146364022 3395233 0.023197182979844595 0.4226647259204529 chr9 141213431 4184154 0.02963000027950599 0.46232312527468317 chr10 135534747 5225384 0.03855383298867264 0.4415914646536795 chr11 135006516 3440776 0.025485999505386835 0.34641948171481485 chr12 133851895 12364319 0.09237313375354156 0.686891365707609 chr13 115169878 62021874 0.5385251341500944 1.741535944617797 chr14 107349540 15080728 0.14048246503897455 1.1158102701735777 chr15 102531392 14138377 0.13789315373773528 0.8564780973532387 chr16 90354753 1471452 0.01628527499820624 0.44482185366828786 chr17 81195210 9690940 0.11935359241019267 0.7943465947000827 chr18 78077248 7615874 0.09754280786126068 3.1231699313631656 chr19 59128983 3299009 0.05579343382246233 0.66333327997268 chr20 63025520 1798822 0.028541168720226346 0.7462002487182939 chr21 48129895 876487 0.01821086457803409 0.27944055298612164 chr22 51304566 602398 0.011741606000526346 0.2119940128776444 chrMT 16571 25370 1.530987870375958 2.842106433006874 chrX 155270560 3878940 0.02498181239251021 0.5160994046938692 chrY 59373566 299651 0.005046875574224395 0.1253605047425344