BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549084.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 = 9,653,152 number of mapped reads = 8,387,707 (86.89%) number of secondary alignments = 0 number of mapped bases = 332,482,437 bp number of sequenced bases = 332,450,265 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 293,421 duplication rate = 1.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6619 >>>>>>> ACTG content number of A's = 100,501,764 bp (30.23%) number of C's = 65,772,811 bp (19.78%) number of T's = 101,838,152 bp (30.63%) number of G's = 64,254,476 bp (19.33%) number of N's = 83,062 bp (0.02%) GC percentage = 39.11% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 1,403,538 number of insertions = 9,226 mapped reads with insertion percentage = 0.11% number of deletions = 26,040 mapped reads with deletion percentage = 0.31% homopolymer indels = 45.05% >>>>>>> Coverage mean coverageData = 0.1074X std coverageData = 0.9235X There is a 9.37% of reference with a coverageData >= 1X There is a 0.98% of reference with a coverageData >= 2X There is a 0.12% 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 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 24766348 0.0993632348863837 2.2864084698722484 chr2 243199373 30969804 0.1273432723858215 0.7686674315267836 chr3 198022430 24092724 0.12166664150116732 0.41384282489361757 chr4 191154276 24288603 0.12706282856052878 0.39216551264044747 chr5 180915260 22269082 0.12309123066788286 0.41261360151254495 chr6 171115067 21599114 0.12622567012173158 0.6196505667891362 chr7 159138663 18136038 0.11396374493858856 0.9273085080826697 chr8 146364022 17964027 0.12273526481801655 0.6481754566858703 chr9 141213431 14336226 0.10152168882576049 0.7376494123090348 chr10 135534747 15753967 0.1162356321807278 0.8831189231390215 chr11 135006516 14334793 0.10617852696828352 0.7603364629068011 chr12 133851895 14430880 0.10781229507434317 0.42427253699759726 chr13 115169878 12938836 0.11234566038178836 0.3573879802910202 chr14 107349540 11115314 0.103543191708134 0.5099873185995536 chr15 102531392 9268978 0.09040136702718325 0.3289062492133998 chr16 90354753 8796402 0.09735405950365444 0.5649254780000922 chr17 81195210 7032293 0.08660970271522175 0.4246068750428428 chr18 78077248 8461801 0.10837729577763806 1.4772182048557934 chr19 59128983 4805447 0.0812705843427072 1.8907603434904332 chr20 63025520 6155237 0.09766261349370858 0.37488941767414047 chr21 48129895 4191376 0.08708466951777061 0.42643723273855455 chr22 51304566 2803061 0.05463570240512316 0.3484184273997494 chrMT 16571 8392 0.5064268903506125 0.8893964041167063 chrX 155270560 11659855 0.07509379112176835 0.5167804599128716 chrY 59373566 2303839 0.03880243608746694 0.29793780950163234