BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818808.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 = 922,167 number of mapped reads = 893,955 (96.94%) number of supplementary alignments = 6,593 (0.71%) number of secondary alignments = 0 number of mapped bases = 60,772,312 bp number of sequenced bases = 60,746,923 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 264,195 duplication rate = 26.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7602 >>>>>>> ACTG content number of A's = 16,614,169 bp (27.35%) number of C's = 12,852,944 bp (21.16%) number of T's = 17,570,402 bp (28.92%) number of G's = 13,705,800 bp (22.56%) number of N's = 3,608 bp (0.01%) GC percentage = 43.72% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 308,917 number of insertions = 6,999 mapped reads with insertion percentage = 0.77% number of deletions = 15,740 mapped reads with deletion percentage = 1.74% homopolymer indels = 43.69% >>>>>>> Coverage mean coverageData = 0.0196X std coverageData = 0.2652X There is a 1.24% of reference with a coverageData >= 1X There is a 0.42% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% 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% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% 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 5018539 0.020134509514421632 0.3329266647665539 chr2 243199373 5387762 0.022153683759702784 0.4294934547940857 chr3 198022430 4092595 0.020667330463523752 0.21187395901770284 chr4 191154276 3987487 0.020860046049924617 0.23130397360985155 chr5 180915260 3768887 0.020832333325558054 0.21863527743227065 chr6 171115067 3614548 0.021123493467702644 0.23331595370412916 chr7 159138663 3315172 0.02083197092085661 0.23953770243575875 chr8 146364022 3108016 0.02123483597628931 0.23211872410167242 chr9 141213431 2628338 0.018612521354289594 0.2317603495162268 chr10 135534747 2912321 0.02148763372096751 0.26969326182187575 chr11 135006516 2869412 0.02125387784986615 0.23392058520864917 chr12 133851895 2774498 0.020728118940714288 0.2187042910862128 chr13 115169878 1928892 0.016748233422631566 0.18855971874785835 chr14 107349540 1873101 0.01744861692001661 0.21495696846168286 chr15 102531392 1764472 0.017209090460802483 0.1940921614432065 chr16 90354753 1796313 0.019880669697586357 0.2902521824822688 chr17 81195210 1646366 0.02027663947171268 0.218298782225693 chr18 78077248 1640675 0.021013483979353372 0.2824010311951069 chr19 59128983 1271409 0.02150229778178326 0.3110073107511779 chr20 63025520 1328506 0.02107885821489454 0.22732196568191054 chr21 48129895 824221 0.01712492828002222 0.2051317270970829 chr22 51304566 753131 0.014679609608236428 0.19684232199790677 chrMT 16571 74328 4.485426347233118 4.758376377893088 chrX 155270560 1861419 0.011988228805254518 0.17387118507892424 chrY 59373566 531904 0.008958599522218355 0.42779813390412574