BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038422.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 18,986,522 number of mapped reads = 17,546,904 (92.42%) number of supplementary alignments = 244,837 (1.29%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,900,018 number of mapped paired reads (second in pair) = 8,646,886 number of mapped paired reads (both in pair) = 17,237,728 number of mapped paired reads (singletons) = 309,176 number of mapped bases = 2,372,040,232 bp number of sequenced bases = 2,370,454,480 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,474,788 duplication rate = 14.34% >>>>>>> Insert size mean insert size = 84,976.1737 std insert size = 2,875,138.4871 median insert size = 248 >>>>>>> Mapping quality mean mapping quality = 53.5237 >>>>>>> ACTG content number of A's = 673,443,448 bp (28.41%) number of C's = 476,918,197 bp (20.12%) number of T's = 682,413,318 bp (28.79%) number of G's = 537,487,232 bp (22.67%) number of N's = 192,285 bp (0.01%) GC percentage = 42.79% >>>>>>> Mismatches and indels general error rate = 0.0128 number of mismatches = 29,402,263 number of insertions = 399,043 mapped reads with insertion percentage = 2.17% number of deletions = 831,282 mapped reads with deletion percentage = 4.57% homopolymer indels = 47.97% >>>>>>> Coverage mean coverageData = 0.7662X std coverageData = 8.859X There is a 27.68% of reference with a coverageData >= 1X There is a 16.55% of reference with a coverageData >= 2X There is a 9.78% of reference with a coverageData >= 3X There is a 6.26% of reference with a coverageData >= 4X There is a 3.99% of reference with a coverageData >= 5X There is a 2.63% of reference with a coverageData >= 6X There is a 1.76% of reference with a coverageData >= 7X There is a 1.2% of reference with a coverageData >= 8X There is a 0.83% of reference with a coverageData >= 9X There is a 0.58% of reference with a coverageData >= 10X There is a 0.41% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.22% of reference with a coverageData >= 13X There is a 0.17% of reference with a coverageData >= 14X There is a 0.13% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% 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 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 212460183 0.8523958020549927 12.294264686805601 chr2 243199373 215087374 0.8844076008370301 10.356670848504718 chr3 198022430 175957846 0.8885753295725136 1.9471801471727537 chr4 191154276 100355594 0.5249979027411346 8.535819719416276 chr5 180915260 165498725 0.9147858782061834 1.9077382875950588 chr6 171115067 119993555 0.7012448237535973 7.0671363305501655 chr7 159138663 115801790 0.7276785403180118 8.521536495207801 chr8 146364022 126018326 0.8609925053849641 3.568149654122603 chr9 141213431 103147952 0.7304400953192618 14.401302463033257 chr10 135534747 145543388 1.0738455726043448 22.35888834892172 chr11 135006516 110335731 0.8172622645858071 7.2124235006272714 chr12 133851895 101000946 0.7545724025797319 1.881960861985633 chr13 115169878 78813178 0.6843211034746429 1.5991503779081062 chr14 107349540 78702392 0.7331413995812185 1.7449345737889368 chr15 102531392 66998700 0.653445727138865 1.6020369387332238 chr16 90354753 75810560 0.839032341773985 8.743648021771671 chr17 81195210 54181630 0.6673008173758034 11.321065492678509 chr18 78077248 95512159 1.2233033495237946 10.0276301425381 chr19 59128983 34796835 0.5884903347652707 5.617498176413102 chr20 63025520 67452725 1.0702446405836874 3.3178471462266725 chr21 48129895 24140019 0.501559768621976 4.130288208274631 chr22 51304566 14785715 0.2881949142694239 1.0179281896964172 chrMT 16571 5928005 357.7336913885704 210.83432843928165 chrX 155270560 79344699 0.5110092924247842 2.034438738848262 chrY 59373566 4372205 0.07363891533818265 8.474041683736429