BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617375.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,004,283 (93.76%) number of supplementary alignments = 65,868 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,077,610 number of mapped paired reads (second in pair) = 14,926,673 number of mapped paired reads (both in pair) = 29,446,224 number of mapped paired reads (singletons) = 558,059 number of mapped bases = 2,941,704,260 bp number of sequenced bases = 2,940,848,709 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,548,930 duplication rate = 1.47% >>>>>>> Insert size mean insert size = 50,455.1772 std insert size = 2,124,350.1838 median insert size = 211 >>>>>>> Mapping quality mean mapping quality = 53.4451 >>>>>>> ACTG content number of A's = 892,483,060 bp (30.35%) number of C's = 582,346,979 bp (19.8%) number of T's = 879,245,274 bp (29.9%) number of G's = 584,596,586 bp (19.88%) number of N's = 2,176,810 bp (0.07%) GC percentage = 39.68% >>>>>>> Mismatches and indels general error rate = 0.0119 number of mismatches = 34,347,963 number of insertions = 293,363 mapped reads with insertion percentage = 0.95% number of deletions = 356,239 mapped reads with deletion percentage = 1.15% homopolymer indels = 41.05% >>>>>>> Coverage mean coverageData = 0.9503X std coverageData = 9.732X There is a 52.71% of reference with a coverageData >= 1X There is a 23.74% of reference with a coverageData >= 2X There is a 9.12% of reference with a coverageData >= 3X There is a 3.21% of reference with a coverageData >= 4X There is a 1.1% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.07% 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 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% 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 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% 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 190610836 0.7647356513506941 19.79650903995695 chr2 243199373 290469007 1.194365772480836 8.737425867686955 chr3 198022430 234266667 1.1830309677545114 1.4906077970546137 chr4 191154276 161659387 0.8457011288620088 9.144049865281698 chr5 180915260 185238511 1.0238965524522365 1.4652880308199976 chr6 171115067 138173775 0.8074904064409477 3.7051817401855103 chr7 159138663 239479310 1.5048468140014473 10.84809739479941 chr8 146364022 124094180 0.8478462008921838 7.598290521360678 chr9 141213431 123913517 0.8774910157094051 14.805794681248026 chr10 135534747 124052245 0.9152800130286886 20.16331113135194 chr11 135006516 157687802 1.1680014170575292 5.526554539678617 chr12 133851895 129911941 0.9705648246519035 1.3489583889689796 chr13 115169878 128871680 1.1189703613300692 1.2921744713010404 chr14 107349540 85163614 0.7933300319684649 1.3867351581192597 chr15 102531392 65881352 0.6425481085831742 0.9700325184247394 chr16 90354753 73616197 0.8147462591148913 7.8812193418110015 chr17 81195210 90679169 1.116804414940241 7.14124663956329 chr18 78077248 53084355 0.6798953134208828 15.12145802142252 chr19 59128983 54026787 0.9137107431731069 9.555115784044343 chr20 63025520 83803465 1.3296751062109444 2.38973709401081 chr21 48129895 46767761 0.9716987955199154 3.188973331073479 chr22 51304566 25714433 0.501211393153584 0.9039905315239782 chrMT 16571 1995309 120.40969162995594 21.261131729130078 chrX 155270560 122556910 0.7893119597172832 2.988824386933302 chrY 59373566 9986050 0.16819016732126213 8.190621889668257