BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085116.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 953,170 number of mapped reads = 711,514 (74.65%) number of supplementary alignments = 5,991 (0.63%) number of secondary alignments = 0 number of mapped bases = 48,664,028 bp number of sequenced bases = 48,650,038 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,983 duplication rate = 1.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6582 >>>>>>> ACTG content number of A's = 15,304,725 bp (31.46%) number of C's = 8,919,867 bp (18.33%) number of T's = 13,905,940 bp (28.58%) number of G's = 10,518,363 bp (21.62%) number of N's = 1,143 bp (0%) GC percentage = 39.96% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 443,603 number of insertions = 3,497 mapped reads with insertion percentage = 0.49% number of deletions = 8,585 mapped reads with deletion percentage = 1.19% homopolymer indels = 44.57% >>>>>>> Coverage mean coverageData = 0.0157X std coverageData = 0.1542X There is a 1.51% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 4388092 0.017605139687896704 0.2306885220986481 chr2 243199373 4663271 0.01917468348078348 0.16712027214583655 chr3 198022430 3055036 0.015427727050920444 0.12795057468764345 chr4 191154276 3103474 0.016235441157486846 0.13045863079173603 chr5 180915260 2574247 0.014229020813390756 0.12169723093018024 chr6 171115067 3377783 0.019739833897853075 0.16297951906176888 chr7 159138663 4135042 0.02598389305306656 0.1872035128134156 chr8 146364022 2879568 0.019674015243992135 0.1991336880361299 chr9 141213431 1570547 0.011121796197983463 0.12918448616803374 chr10 135534747 3194855 0.023572220930179626 0.2059351739305027 chr11 135006516 2117920 0.0156875391110752 0.1493837238378313 chr12 133851895 2046029 0.015285767900409628 0.12650697437148534 chr13 115169878 1058554 0.009191240091441271 0.09713457465773716 chr14 107349540 1569428 0.014619792502138343 0.12499174077939214 chr15 102531392 846681 0.008257773385150179 0.09220279440534154 chr16 90354753 1224969 0.013557327747882836 0.12311303148986286 chr17 81195210 751472 0.009255127242111942 0.10311312627999152 chr18 78077248 1267103 0.016228837881171222 0.20248382793278386 chr19 59128983 677006 0.011449647290568146 0.1557258192345285 chr20 63025520 1085791 0.017227799151835636 0.13392405488209122 chr21 48129895 560878 0.011653422472664859 0.11288531715174555 chr22 51304566 300854 0.005864078452588411 0.07785790173246211 chrMT 16571 6887 0.415605576006276 0.6861015650061437 chrX 155270560 2118572 0.013644389509511655 0.12451321529663979 chrY 59373566 89969 0.0015153039654044024 0.04514262089309482