BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081738.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 = 2,247,736 number of mapped reads = 1,991,031 (88.58%) number of supplementary alignments = 18,610 (0.83%) number of secondary alignments = 0 number of mapped bases = 130,556,076 bp number of sequenced bases = 130,503,462 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,830 duplication rate = 2.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2965 >>>>>>> ACTG content number of A's = 36,225,510 bp (27.76%) number of C's = 25,262,256 bp (19.36%) number of T's = 39,423,796 bp (30.21%) number of G's = 29,590,403 bp (22.67%) number of N's = 1,497 bp (0%) GC percentage = 42.03% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,110,189 number of insertions = 10,544 mapped reads with insertion percentage = 0.52% number of deletions = 29,781 mapped reads with deletion percentage = 1.48% homopolymer indels = 45.74% >>>>>>> Coverage mean coverageData = 0.0422X std coverageData = 0.3937X There is a 3.68% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% 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% 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 10376557 0.04163101764147661 0.67749250981593 chr2 243199373 11096017 0.04562518752875239 0.511664668800745 chr3 198022430 8689370 0.04388073613681036 0.23418465296413865 chr4 191154276 8493892 0.04443474756484129 0.2730688279859841 chr5 180915260 7931091 0.04383870658561362 0.2332979794104056 chr6 171115067 7557100 0.044163849113298716 0.2759608101377282 chr7 159138663 7243261 0.04551540690020753 0.5462340946241133 chr8 146364022 6583438 0.04497989266788528 0.5046023752063236 chr9 141213431 5390298 0.03817128414647754 0.36223547317778193 chr10 135534747 6226795 0.04594242537671908 0.4299924304964811 chr11 135006516 5867858 0.04346351697572878 0.33592919506937036 chr12 133851895 5927374 0.044283078696793945 0.2368313034578524 chr13 115169878 4066408 0.0353079127165525 0.20780079559075365 chr14 107349540 3980173 0.037076758782571405 0.23743354895997512 chr15 102531392 3725119 0.03633149738179698 0.21924583494380415 chr16 90354753 3747530 0.04147573730847341 0.2718270668465085 chr17 81195210 3572705 0.044001425699865794 0.25061516542941126 chr18 78077248 3492113 0.04472638431108637 0.6748074424778115 chr19 59128983 2848410 0.0481728224549372 0.5323164667434949 chr20 63025520 2617583 0.04153211270609112 0.23717854678846093 chr21 48129895 1705956 0.03544483111795694 0.23875781000811766 chr22 51304566 1487394 0.02899145467871222 0.1880866405471401 chrMT 16571 9052 0.5462555066079295 0.790970543936872 chrX 155270560 7528401 0.04848569490571812 0.2834534233471754 chrY 59373566 392181 0.006605313212954061 0.17675313801382497