BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084389.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,261,608 number of mapped reads = 2,024,090 (89.5%) number of supplementary alignments = 13,586 (0.6%) number of secondary alignments = 0 number of mapped bases = 134,909,780 bp number of sequenced bases = 134,862,468 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,054 duplication rate = 2.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.0622 >>>>>>> ACTG content number of A's = 37,780,780 bp (28.01%) number of C's = 25,591,352 bp (18.98%) number of T's = 41,514,465 bp (30.78%) number of G's = 29,802,381 bp (22.1%) number of N's = 173,490 bp (0.13%) GC percentage = 41.07% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 1,363,082 number of insertions = 9,863 mapped reads with insertion percentage = 0.48% number of deletions = 27,180 mapped reads with deletion percentage = 1.33% homopolymer indels = 46.33% >>>>>>> Coverage mean coverageData = 0.0436X std coverageData = 0.3111X There is a 3.77% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% 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 17270459 0.06928953248224806 0.5568123540781212 chr2 243199373 14473203 0.05951167892196827 0.34593580935166895 chr3 198022430 9739285 0.049182736521312255 0.25085652851016843 chr4 191154276 3902003 0.020412847055537486 0.17183651044793632 chr5 180915260 3803312 0.021022615781554302 0.16214747486565545 chr6 171115067 6383532 0.037305493384752614 0.22798119618141352 chr7 159138663 5916555 0.037178614476608994 0.3630943974303485 chr8 146364022 10773662 0.07360867686459177 0.3925152644909806 chr9 141213431 4145541 0.02935656311615288 0.22720805028013427 chr10 135534747 9757521 0.07199276359736739 0.43732366839145015 chr11 135006516 7763827 0.05750705395582536 0.32944939121200595 chr12 133851895 4162425 0.031097243711043464 0.19635687512214922 chr13 115169878 4155833 0.03608437442297195 0.2102181344395265 chr14 107349540 3504728 0.03264781572422201 0.20486186205554027 chr15 102531392 3674078 0.03583368886672288 0.21994928341476375 chr16 90354753 2537760 0.028086624286383696 0.21111198301806983 chr17 81195210 4622111 0.056925907328769766 0.28848975553367406 chr18 78077248 473909 0.006069745183641719 0.3314644679151658 chr19 59128983 2893501 0.04893540956048576 0.36964051746858817 chr20 63025520 2123739 0.03369649310311125 0.20712476303569377 chr21 48129895 1757870 0.036523453874146204 0.2233259579635497 chr22 51304566 988308 0.019263548589417947 0.15204076603002425 chrMT 16571 11979 0.7228893850703035 0.950795988376619 chrX 155270560 9748008 0.06278078729155095 0.3079728314098703 chrY 59373566 326631 0.005501286548966926 0.11399897365156932