BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549005.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 11,051,335 number of mapped reads = 9,522,912 (86.17%) number of secondary alignments = 0 number of mapped bases = 378,065,941 bp number of sequenced bases = 378,023,727 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 885,298 duplication rate = 8.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6774 >>>>>>> ACTG content number of A's = 114,386,412 bp (30.26%) number of C's = 74,051,311 bp (19.59%) number of T's = 114,611,601 bp (30.32%) number of G's = 74,970,639 bp (19.83%) number of N's = 3,764 bp (0%) GC percentage = 39.42% >>>>>>> Mismatches and indels general error rate = 0.0029 number of mismatches = 1,090,723 number of insertions = 11,919 mapped reads with insertion percentage = 0.13% number of deletions = 32,793 mapped reads with deletion percentage = 0.34% homopolymer indels = 44.19% >>>>>>> Coverage mean coverageData = 0.1221X std coverageData = 1.1109X There is a 8.44% of reference with a coverageData >= 1X There is a 2.45% of reference with a coverageData >= 2X There is a 0.75% of reference with a coverageData >= 3X There is a 0.25% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 30648466 0.12296244589898134 1.4340435003379688 chr2 243199373 32658409 0.1342865674246619 0.6561023740515719 chr3 198022430 26460105 0.13362175688885344 0.490303122292859 chr4 191154276 26750821 0.1399436181066648 0.5444614656048226 chr5 180915260 25034493 0.13837690087613394 0.5072117745818373 chr6 171115067 22460117 0.13125738950854632 0.5499642052879342 chr7 159138663 21155165 0.13293541997396321 0.9110877910988806 chr8 146364022 20384014 0.13926929392525167 3.93791813134861 chr9 141213431 16231597 0.11494371948232035 0.6113394842514209 chr10 135534747 18079681 0.1333951728260503 0.6983912222377142 chr11 135006516 17175910 0.1272228223414046 0.6112161651332607 chr12 133851895 17447707 0.13035084038220004 0.5080446568180261 chr13 115169878 13035191 0.113182294071719 0.45019420580095637 chr14 107349540 11769887 0.10964077722177477 0.534310532843927 chr15 102531392 10782378 0.10516172451847723 0.4293164004474752 chr16 90354753 9990976 0.11057499100241025 0.48544440419837415 chr17 81195210 9016433 0.11104636591247193 0.47763765371208955 chr18 78077248 10508638 0.13459283298509703 1.2069322720990157 chr19 59128983 6183080 0.10456936152614023 1.1078016111088265 chr20 63025520 7432677 0.11793122849283909 0.4902817011996393 chr21 48129895 5097628 0.10591396469907113 0.5307205762656716 chr22 51304566 3737112 0.07284170379689013 0.40267709971426024 chrMT 16571 7064 0.42628688672982923 0.8527700688373031 chrX 155270560 12593349 0.0811058387372339 0.48256851968067044 chrY 59373566 3425043 0.05768632795274584 0.6069507667854623