BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818796.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,607,862 number of mapped reads = 1,569,480 (97.61%) number of supplementary alignments = 10,925 (0.68%) number of secondary alignments = 0 number of mapped bases = 106,715,101 bp number of sequenced bases = 106,670,696 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 726,994 duplication rate = 37.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6078 >>>>>>> ACTG content number of A's = 29,988,003 bp (28.11%) number of C's = 24,514,142 bp (22.98%) number of T's = 28,717,165 bp (26.92%) number of G's = 23,445,306 bp (21.98%) number of N's = 6,080 bp (0.01%) GC percentage = 44.96% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 556,602 number of insertions = 11,753 mapped reads with insertion percentage = 0.74% number of deletions = 27,478 mapped reads with deletion percentage = 1.73% homopolymer indels = 41.68% >>>>>>> Coverage mean coverageData = 0.0345X std coverageData = 0.4862X There is a 1.61% of reference with a coverageData >= 1X There is a 0.74% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 8928806 0.03582260282512997 0.6406689239610418 chr2 243199373 9205352 0.03785105153211065 0.8496576236057609 chr3 198022430 7142689 0.03607010074565795 0.36023408855601313 chr4 191154276 6939617 0.03630374975237279 0.4144978152373655 chr5 180915260 6672244 0.03688049311042087 0.37671821285060453 chr6 171115067 6215615 0.03632418295461965 0.40031391716796866 chr7 159138663 5873283 0.03690670066770638 0.4225423879047783 chr8 146364022 5460063 0.03730467997114755 0.390569461799413 chr9 141213431 4675653 0.03311054031397339 0.40728934984504733 chr10 135534747 5195822 0.038335719179082545 0.5120291233399982 chr11 135006516 4973050 0.03683562947435811 0.4029977136329942 chr12 133851895 4918758 0.03674776513249962 0.39424225267847307 chr13 115169878 3379224 0.02934121368088972 0.3229362021215842 chr14 107349540 3311126 0.030844342695832697 0.36214260216807775 chr15 102531392 3111199 0.03034386775905666 0.3306887808786972 chr16 90354753 3253887 0.03601235011953383 0.5412902192737585 chr17 81195210 2974101 0.03662902035723536 0.38727903814806314 chr18 78077248 2844290 0.03642917844645344 0.47760519483827624 chr19 59128983 2221698 0.0375737563421309 0.54292040914719 chr20 63025520 2385352 0.03784739895839019 0.39463895148282807 chr21 48129895 1431720 0.02974700027914044 0.33606829421034173 chr22 51304566 1346300 0.026241329085602245 0.3443267912461668 chrMT 16571 32530 1.9630680103795788 3.1525747947886122 chrX 155270560 3227358 0.02078538262501275 0.30833208679839647 chrY 59373566 995364 0.016764430150616186 0.8427650193624314