BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124940.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 2,092,458 number of mapped reads = 2,057,439 (98.33%) number of supplementary alignments = 33,913 (1.62%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,029,286 number of mapped paired reads (second in pair) = 1,028,153 number of mapped paired reads (both in pair) = 2,046,388 number of mapped paired reads (singletons) = 11,051 number of mapped bases = 274,919,118 bp number of sequenced bases = 274,700,357 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 329,347 duplication rate = 15.61% >>>>>>> Insert size mean insert size = 82,152.9724 std insert size = 2,725,616.5945 median insert size = 167 >>>>>>> Mapping quality mean mapping quality = 53.5432 >>>>>>> ACTG content number of A's = 80,284,173 bp (29.23%) number of C's = 55,211,640 bp (20.1%) number of T's = 80,597,719 bp (29.34%) number of G's = 58,586,490 bp (21.33%) number of N's = 20,335 bp (0.01%) GC percentage = 41.43% >>>>>>> Mismatches and indels general error rate = 0.0118 number of mismatches = 3,105,646 number of insertions = 57,109 mapped reads with insertion percentage = 2.62% number of deletions = 108,823 mapped reads with deletion percentage = 5.07% homopolymer indels = 45.4% >>>>>>> Coverage mean coverageData = 0.0888X std coverageData = 0.9983X There is a 5.04% of reference with a coverageData >= 1X There is a 2.82% of reference with a coverageData >= 2X There is a 0.36% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% 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 18194867 0.07299828151681917 0.8508157484971058 chr2 243199373 25784731 0.10602301593927217 1.5048337507408258 chr3 198022430 25962104 0.13110688521497288 0.5134014725183186 chr4 191154276 18901249 0.09887955109097324 0.818248433027664 chr5 180915260 14077835 0.0778145248775587 0.39050587599892206 chr6 171115067 15896552 0.0928997795384085 0.7025793121384536 chr7 159138663 13166200 0.08273413733531242 0.9196230090074697 chr8 146364022 17708757 0.12099118866793644 0.5839077287626251 chr9 141213431 11429323 0.08093651516759762 1.5380948053640677 chr10 135534747 15609919 0.11517281985260945 2.2965319994684688 chr11 135006516 11660368 0.08636892755605959 0.759649289600718 chr12 133851895 12155432 0.0908125506926891 0.4177449760685756 chr13 115169878 5733907 0.04978651622779352 0.30439283931163635 chr14 107349540 9223022 0.0859158036448037 0.4231887358288522 chr15 102531392 5490094 0.053545493657201106 0.31730610734914905 chr16 90354753 10833844 0.11990342112937877 1.6594881741140886 chr17 81195210 7075748 0.0871448943847796 0.8065247509466934 chr18 78077248 5474341 0.07011442052875634 1.4481374067405681 chr19 59128983 2984454 0.05047362306231447 0.6277202023882915 chr20 63025520 6185659 0.09814530685347776 0.4820816327769963 chr21 48129895 4008720 0.08328960617927797 0.572548754691533 chr22 51304566 2118040 0.041283654947982605 0.2931038460712842 chrMT 16571 187555 11.318266851728923 7.056404763556543 chrX 155270560 11445825 0.0737153585328732 0.4431354653382324 chrY 59373566 3610572 0.06081110236835025 1.4728483710113762