BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714120.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 850,600 number of mapped reads = 325,332 (38.25%) number of supplementary alignments = 15,833 (1.86%) number of secondary alignments = 0 number of mapped bases = 40,450,106 bp number of sequenced bases = 39,788,957 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 277,694 duplication rate = 42.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.6212 >>>>>>> ACTG content number of A's = 10,287,535 bp (25.86%) number of C's = 7,126,929 bp (17.91%) number of T's = 9,732,853 bp (24.46%) number of G's = 12,641,135 bp (31.77%) number of N's = 505 bp (0%) GC percentage = 49.68% >>>>>>> Mismatches and indels general error rate = 0.04 number of mismatches = 1,415,053 number of insertions = 47,934 mapped reads with insertion percentage = 13.69% number of deletions = 110,237 mapped reads with deletion percentage = 32.47% homopolymer indels = 28.58% >>>>>>> Coverage mean coverageData = 0.0131X std coverageData = 6.7764X There is a 0.05% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.03% 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 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 0.01% 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 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% 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 1700144 0.006821022122949896 0.8691544217174578 chr2 243199373 8197378 0.03370641091249853 23.10552271250793 chr3 198022430 2540554 0.012829627431599542 2.8855410070868217 chr4 191154276 3271487 0.017114380428507915 3.659334840069473 chr5 180915260 1927153 0.010652241275832674 1.992851026713569 chr6 171115067 1895419 0.011076867941734202 2.090152623313289 chr7 159138663 1504608 0.009454698007611137 1.4023134938178625 chr8 146364022 1295029 0.008848000911043562 0.8989331978353734 chr9 141213431 1402130 0.009929154685010096 1.578766564104809 chr10 135534747 1482431 0.010937645384766166 1.3344899929154508 chr11 135006516 1841119 0.01363726029342169 1.687156068242436 chr12 133851895 2062550 0.015409195364772385 3.4840751265540684 chr13 115169878 697782 0.00605871962458795 0.6394196154100332 chr14 107349540 802172 0.007472523869221983 0.8293542088612694 chr15 102531392 759790 0.0074103158572157105 0.8707787788830879 chr16 90354753 909020 0.010060566487299236 1.3515804326464422 chr17 81195210 724741 0.00892590831404956 1.0904324333271944 chr18 78077248 919978 0.011782920422605059 1.3082401086321516 chr19 59128983 759412 0.012843312390473552 2.1535146327952845 chr20 63025520 570955 0.009059108120012338 1.0426949748170864 chr21 48129895 210237 0.004368116739087006 0.6703978667639741 chr22 51304566 324001 0.006315246872958637 0.6502714619693499 chrMT 16571 605806 36.55820409148512 295.33563214557097 chrX 155270560 3801130 0.024480687130902342 2.4807638508804333 chrY 59373566 245080 0.004127762849885082 0.552283823108135