BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472490.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 185,840 number of mapped reads = 183,386 (98.68%) number of supplementary alignments = 743 (0.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 92,146 number of mapped paired reads (second in pair) = 91,240 number of mapped paired reads (both in pair) = 182,022 number of mapped paired reads (singletons) = 1,364 number of mapped bases = 18,051,224 bp number of sequenced bases = 18,048,817 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,755 duplication rate = 15% >>>>>>> Insert size mean insert size = 32,044.0937 std insert size = 1,860,945.9732 median insert size = 235 >>>>>>> Mapping quality mean mapping quality = 55.0732 >>>>>>> ACTG content number of A's = 4,999,099 bp (27.7%) number of C's = 4,047,291 bp (22.42%) number of T's = 4,976,863 bp (27.57%) number of G's = 4,022,867 bp (22.29%) number of N's = 2,697 bp (0.01%) GC percentage = 44.71% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 108,636 number of insertions = 1,010 mapped reads with insertion percentage = 0.55% number of deletions = 923 mapped reads with deletion percentage = 0.49% homopolymer indels = 44.85% >>>>>>> Coverage mean coverageData = 0.0058X std coverageData = 0.1569X There is a 0.26% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.04% 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% 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 1918965 0.007698937688905497 0.20588015414423752 chr2 243199373 1301349 0.005350955407274015 0.15448310978217764 chr3 198022430 2071295 0.01045990093142479 0.20056799571567335 chr4 191154276 738362 0.003862649664190614 0.12411787010172178 chr5 180915260 949046 0.005245804030019358 0.14825474931290442 chr6 171115067 1177887 0.006883596054110186 0.16292503830390476 chr7 159138663 749353 0.004708805427126154 0.13155940860808812 chr8 146364022 824064 0.005630236097228867 0.15092460068448896 chr9 141213431 1104796 0.007823590094627755 0.17490850969979035 chr10 135534747 490309 0.0036175889272143623 0.12612826333307708 chr11 135006516 807351 0.005980089138808678 0.16177964559271957 chr12 133851895 918308 0.006860627561529853 0.17622367043690648 chr13 115169878 423726 0.00367913908878153 0.11882470353373144 chr14 107349540 475580 0.004430200632438667 0.15354311183733188 chr15 102531392 471542 0.004599001250270746 0.13971041485406013 chr16 90354753 594678 0.006581590677360382 0.16415038519156994 chr17 81195210 658183 0.008106180155208663 0.17314257453790277 chr18 78077248 310173 0.003972642580845062 0.12979092478246282 chr19 59128983 384320 0.006499688993467045 0.16775596958141425 chr20 63025520 361020 0.005728155832748385 0.1454043631744463 chr21 48129895 75225 0.0015629579079696726 0.06492462151751655 chr22 51304566 173477 0.0033813169767384836 0.10049006150173126 chrMT 16571 362 0.021845392553255686 0.173024155861544 chrX 155270560 1036642 0.006676358995549446 0.15999849356108659 chrY 59373566 35211 5.930416913142795E-4 0.03607173854430079