BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708644.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 4,202,992 number of mapped reads = 4,020,701 (95.66%) number of supplementary alignments = 122 (0%) number of secondary alignments = 0 number of mapped bases = 200,536,682 bp number of sequenced bases = 200,516,599 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,489 duplication rate = 0.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5996 >>>>>>> ACTG content number of A's = 62,002,591 bp (30.92%) number of C's = 38,088,571 bp (19%) number of T's = 61,954,588 bp (30.9%) number of G's = 38,464,033 bp (19.18%) number of N's = 6,816 bp (0%) GC percentage = 38.18% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 328,943 number of insertions = 13,787 mapped reads with insertion percentage = 0.34% number of deletions = 11,648 mapped reads with deletion percentage = 0.29% homopolymer indels = 49.13% >>>>>>> Coverage mean coverageData = 0.0648X std coverageData = 0.2637X There is a 6.07% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.03% 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 14942822 0.05995099205790946 0.2543505332994806 chr2 243199373 18909489 0.07775303351625006 0.28838051119026326 chr3 198022430 14771137 0.0745932518856576 0.28169922751880705 chr4 191154276 14173595 0.07414741274215597 0.2799527243662762 chr5 180915260 12383761 0.06845061605085165 0.2690925077820295 chr6 171115067 14451763 0.08445640266149093 0.30050909634545936 chr7 159138663 12397676 0.07790486463996496 0.2894163823444529 chr8 146364022 8719848 0.05957644427125677 0.25039116781924436 chr9 141213431 8681643 0.061478875900975734 0.25696950313332334 chr10 135534747 8747477 0.06454047536606979 0.2617659137811556 chr11 135006516 9028684 0.06687591286334654 0.2681381830098041 chr12 133851895 9180921 0.0685901458473935 0.27078782742656077 chr13 115169878 8252387 0.07165403960921102 0.27722440153217537 chr14 107349540 6660371 0.06204377773765961 0.2587668437725115 chr15 102531392 6010898 0.058624952638895216 0.253012475623605 chr16 90354753 4247615 0.047010421244801585 0.22435306019851975 chr17 81195210 3257651 0.040121221436584746 0.20721979262811316 chr18 78077248 8995229 0.11520935010414302 0.35292025087762446 chr19 59128983 1942578 0.032853228678057934 0.18707270687111027 chr20 63025520 3131426 0.04968504821538958 0.22992144073044152 chr21 48129895 2730054 0.056722625303878185 0.2476072831352744 chr22 51304566 1374793 0.026796698757767485 0.16976322843636968 chrMT 16571 246 0.014845211514090881 0.12093316835836554 chrX 155270560 6533544 0.04207844680923415 0.21038462358291002 chrY 59373566 1011074 0.017029026014708296 0.13483564110364496