BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153391.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 33,131,220 number of mapped reads = 32,910,554 (99.33%) number of supplementary alignments = 255,549 (0.77%) number of secondary alignments = 0 number of mapped bases = 3,197,089,183 bp number of sequenced bases = 3,196,483,202 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,999,416 duplication rate = 28.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.538 >>>>>>> ACTG content number of A's = 861,937,924 bp (26.97%) number of C's = 732,207,538 bp (22.91%) number of T's = 879,227,219 bp (27.51%) number of G's = 721,929,834 bp (22.59%) number of N's = 1,180,687 bp (0.04%) GC percentage = 45.49% >>>>>>> Mismatches and indels general error rate = 0.0027 number of mismatches = 8,181,444 number of insertions = 339,551 mapped reads with insertion percentage = 1.02% number of deletions = 283,837 mapped reads with deletion percentage = 0.85% homopolymer indels = 49.87% >>>>>>> Coverage mean coverageData = 1.0328X std coverageData = 9.6825X There is a 18.62% of reference with a coverageData >= 1X There is a 9.11% of reference with a coverageData >= 2X There is a 4.88% of reference with a coverageData >= 3X There is a 3.55% of reference with a coverageData >= 4X There is a 2.8% of reference with a coverageData >= 5X There is a 2.41% of reference with a coverageData >= 6X There is a 2.14% of reference with a coverageData >= 7X There is a 1.95% of reference with a coverageData >= 8X There is a 1.8% of reference with a coverageData >= 9X There is a 1.67% of reference with a coverageData >= 10X There is a 1.56% of reference with a coverageData >= 11X There is a 1.47% of reference with a coverageData >= 12X There is a 1.38% of reference with a coverageData >= 13X There is a 1.31% of reference with a coverageData >= 14X There is a 1.24% of reference with a coverageData >= 15X There is a 1.18% of reference with a coverageData >= 16X There is a 1.13% of reference with a coverageData >= 17X There is a 1.08% of reference with a coverageData >= 18X There is a 1.03% of reference with a coverageData >= 19X There is a 0.98% of reference with a coverageData >= 20X There is a 0.94% of reference with a coverageData >= 21X There is a 0.91% of reference with a coverageData >= 22X There is a 0.87% of reference with a coverageData >= 23X There is a 0.84% of reference with a coverageData >= 24X There is a 0.81% of reference with a coverageData >= 25X There is a 0.78% of reference with a coverageData >= 26X There is a 0.75% of reference with a coverageData >= 27X There is a 0.72% of reference with a coverageData >= 28X There is a 0.7% of reference with a coverageData >= 29X There is a 0.68% of reference with a coverageData >= 30X There is a 0.65% of reference with a coverageData >= 31X There is a 0.63% of reference with a coverageData >= 32X There is a 0.61% of reference with a coverageData >= 33X There is a 0.6% of reference with a coverageData >= 34X There is a 0.58% of reference with a coverageData >= 35X There is a 0.56% of reference with a coverageData >= 36X There is a 0.54% of reference with a coverageData >= 37X There is a 0.53% of reference with a coverageData >= 38X There is a 0.51% of reference with a coverageData >= 39X There is a 0.5% of reference with a coverageData >= 40X There is a 0.48% of reference with a coverageData >= 41X There is a 0.47% of reference with a coverageData >= 42X There is a 0.46% of reference with a coverageData >= 43X There is a 0.45% of reference with a coverageData >= 44X There is a 0.43% of reference with a coverageData >= 45X There is a 0.42% of reference with a coverageData >= 46X There is a 0.41% of reference with a coverageData >= 47X There is a 0.4% of reference with a coverageData >= 48X There is a 0.39% of reference with a coverageData >= 49X There is a 0.38% of reference with a coverageData >= 50X There is a 0.37% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 337878085 1.35557569984951 11.887889006208542 chr2 243199373 258178568 1.0615922434964502 9.030513078378723 chr3 198022430 184510579 0.931766058016761 8.441658136187762 chr4 191154276 148972452 0.7793309944057961 7.102148151615646 chr5 180915260 177137155 0.9791167146430876 9.206034232799649 chr6 171115067 179458293 1.048757985759372 9.438924252527176 chr7 159138663 160303536 1.007319861673087 9.268569964115859 chr8 146364022 131302007 0.8970920941213272 10.185895440947657 chr9 141213431 132889262 0.9410525688594026 10.015859821607442 chr10 135534747 143154701 1.0562214057181956 9.001115062830381 chr11 135006516 155160361 1.1492805354668956 9.611159482909992 chr12 133851895 160970238 1.2025996195272395 9.587846723207045 chr13 115169878 78073527 0.6778988426123018 9.875060509059589 chr14 107349540 91065704 0.8483101464617361 7.468573384302494 chr15 102531392 120531354 1.1755556191024892 10.414951938541732 chr16 90354753 103783091 1.1486179481891783 9.028054756243572 chr17 81195210 123330113 1.5189333582609121 11.072574087658952 chr18 78077248 65269286 0.8359578196198718 7.786779873316741 chr19 59128983 131009973 2.2156642369445114 18.481345523221947 chr20 63025520 61420466 0.974533268428408 8.909341810159873 chr21 48129895 26358334 0.5476499377362033 5.039048335996533 chr22 51304566 42399193 0.8264214339129192 7.709520894397965 chrMT 16571 4766 0.2876108864884437 1.0116341439008927 chrX 155270560 181858504 1.1712362214704448 11.858717304326895 chrY 59373566 2069635 0.03485785239848993 1.3324389768447256