BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054577.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 7,912,350 number of mapped reads = 5,045,957 (63.77%) number of supplementary alignments = 179 (0%) number of secondary alignments = 0 number of mapped bases = 236,722,075 bp number of sequenced bases = 236,676,661 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,225,801 duplication rate = 20.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1788 >>>>>>> ACTG content number of A's = 70,378,544 bp (29.74%) number of C's = 46,786,526 bp (19.77%) number of T's = 69,361,610 bp (29.31%) number of G's = 50,078,033 bp (21.16%) number of N's = 71,948 bp (0.03%) GC percentage = 40.93% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 1,650,898 number of insertions = 10,416 mapped reads with insertion percentage = 0.21% number of deletions = 31,113 mapped reads with deletion percentage = 0.62% homopolymer indels = 46.32% >>>>>>> Coverage mean coverageData = 0.0765X std coverageData = 0.6505X There is a 3.65% of reference with a coverageData >= 1X There is a 1.49% of reference with a coverageData >= 2X There is a 0.79% of reference with a coverageData >= 3X There is a 0.48% of reference with a coverageData >= 4X There is a 0.31% of reference with a coverageData >= 5X There is a 0.21% of reference with a coverageData >= 6X There is a 0.15% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% 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 0.01% 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 21594805 0.0866389215535796 0.7208705264600378 chr2 243199373 21493224 0.08837697126793168 0.8993895944774629 chr3 198022430 15687996 0.0792233283875973 0.6031222718283581 chr4 191154276 11488929 0.06010291394161646 0.5180496685362139 chr5 180915260 13571745 0.0750171378578015 0.5837609092212717 chr6 171115067 14607245 0.08536504269375647 0.6693419303092789 chr7 159138663 12331313 0.07748785095674707 0.6924483853535759 chr8 146364022 13989884 0.0955828065451768 0.7185471699686208 chr9 141213431 12437556 0.08807629636872147 0.6624597882054468 chr10 135534747 8354262 0.06163926361997783 0.571071184012057 chr11 135006516 10053221 0.07446470954038989 0.6348051685961194 chr12 133851895 12756637 0.09530411952703396 0.6762885214741167 chr13 115169878 6547545 0.056851193330256025 0.5262856881561154 chr14 107349540 4685932 0.04365116049868495 0.4896294376815519 chr15 102531392 6120938 0.05969818492272103 0.5109011319778927 chr16 90354753 5856667 0.06481858237164347 0.5692756121008671 chr17 81195210 5561850 0.06849973046439563 0.5581983623731972 chr18 78077248 7362549 0.09429826471342842 0.7368969536932444 chr19 59128983 4823254 0.08157173953084902 0.6707412883697981 chr20 63025520 5247127 0.08325400567896941 0.6354877979986132 chr21 48129895 2723598 0.05658848829817725 0.5333462986772652 chr22 51304566 3375925 0.06580164814180477 0.5511961575390666 chrMT 16571 21793 1.3151288395389535 2.5877315070077187 chrX 155270560 15448768 0.0994957962410904 0.7260842283817944 chrY 59373566 579312 0.009757069332840814 0.21691047381832346