BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080678.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 = 1,432,663 number of mapped reads = 1,314,091 (91.72%) number of supplementary alignments = 12,755 (0.89%) number of secondary alignments = 0 number of mapped bases = 87,125,106 bp number of sequenced bases = 87,093,539 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,831 duplication rate = 3.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8683 >>>>>>> ACTG content number of A's = 23,840,939 bp (27.37%) number of C's = 15,900,832 bp (18.26%) number of T's = 27,820,731 bp (31.94%) number of G's = 19,527,152 bp (22.42%) number of N's = 3,885 bp (0%) GC percentage = 40.68% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 586,402 number of insertions = 6,571 mapped reads with insertion percentage = 0.5% number of deletions = 19,884 mapped reads with deletion percentage = 1.5% homopolymer indels = 48.74% >>>>>>> Coverage mean coverageData = 0.0281X std coverageData = 0.2235X There is a 2.43% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% 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 10621846 0.04261512351457692 0.2667947504485333 chr2 243199373 5895522 0.024241518089769088 0.31669523654594367 chr3 198022430 5462833 0.027586940529918755 0.1868875371353932 chr4 191154276 3637597 0.019029639703168344 0.15803387477914685 chr5 180915260 4017992 0.022209248683610214 0.16635899608232724 chr6 171115067 5240897 0.030627910749671156 0.22973700612732267 chr7 159138663 5367153 0.03372626675894594 0.35598518185628775 chr8 146364022 10475399 0.07157086049466446 0.33006873974074663 chr9 141213431 2804983 0.01986342927961293 0.17397693078692042 chr10 135534747 4073279 0.030053392876440755 0.2034123517049399 chr11 135006516 3672041 0.02719899089907631 0.193989104816815 chr12 133851895 2816906 0.0210449467301154 0.16363084962394142 chr13 115169878 1862055 0.016167899387720112 0.14305529050364557 chr14 107349540 1582620 0.014742680779069943 0.13671338161596774 chr15 102531392 1571189 0.015323979996292257 0.14733902844870145 chr16 90354753 2160814 0.023914779557861223 0.1762322956612907 chr17 81195210 1412472 0.017396001562161117 0.15052585512348868 chr18 78077248 2750265 0.03522492237431319 0.24581851936826482 chr19 59128983 1411287 0.023867939687039774 0.19187710901463162 chr20 63025520 2251059 0.035716627169438665 0.21481102416413497 chr21 48129895 1248323 0.025936541104026926 0.1822392641449644 chr22 51304566 802107 0.015634222497857207 0.13910871237899913 chrMT 16571 9463 0.5710578721863496 0.949683480869696 chrX 155270560 5810827 0.03742388125604751 0.2225381292919547 chrY 59373566 166177 0.00279883812267567 0.06128818542187094