BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080721.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 = 2,764,217 number of mapped reads = 2,566,964 (92.86%) number of supplementary alignments = 12,862 (0.47%) number of secondary alignments = 0 number of mapped bases = 179,561,849 bp number of sequenced bases = 179,492,192 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 108,704 duplication rate = 3.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.012 >>>>>>> ACTG content number of A's = 52,433,194 bp (29.21%) number of C's = 33,169,161 bp (18.48%) number of T's = 57,146,159 bp (31.84%) number of G's = 36,741,018 bp (20.47%) number of N's = 2,660 bp (0%) GC percentage = 38.95% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,437,399 number of insertions = 13,476 mapped reads with insertion percentage = 0.52% number of deletions = 38,801 mapped reads with deletion percentage = 1.5% homopolymer indels = 48.45% >>>>>>> Coverage mean coverageData = 0.058X std coverageData = 0.4936X There is a 4.79% of reference with a coverageData >= 1X There is a 0.74% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% 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 22368883 0.08974454270266392 0.7716761208326537 chr2 243199373 12391157 0.05095061244257402 0.42713581171095427 chr3 198022430 10638957 0.05372601982512789 0.2718941763483103 chr4 191154276 8360936 0.043739204662102356 0.24929243741875723 chr5 180915260 8434639 0.046622042828227975 0.2473824169128935 chr6 171115067 10901147 0.0637065291275607 0.418174451051926 chr7 159138663 11996272 0.0753825109112548 1.285510566327335 chr8 146364022 22008949 0.15037130504653665 0.7325023089498345 chr9 141213431 5382017 0.038112642415720356 0.3182978196550253 chr10 135534747 8705029 0.06422728630614553 0.4490316456915618 chr11 135006516 6578106 0.04872435934869988 0.28861379827290784 chr12 133851895 5871279 0.04386399609807541 0.24043425666352836 chr13 115169878 3929135 0.03411599515630293 0.2100997397724212 chr14 107349540 3394154 0.031617778706830045 0.21244654180773173 chr15 102531392 3286099 0.032049686792509365 0.20440549639493438 chr16 90354753 4132897 0.04574078133997002 0.2736200205368186 chr17 81195210 2597003 0.03198468234764095 0.21198384065049136 chr18 78077248 4639800 0.05942576254736847 0.5144211054337778 chr19 59128983 2695210 0.04558187648855723 0.4570449800202569 chr20 63025520 4287820 0.06803307612535367 0.3034273787452144 chr21 48129895 2192496 0.04555372497696079 0.252959812996873 chr22 51304566 1551110 0.030233371431306912 0.1966764160853866 chrMT 16571 16352 0.986784140969163 1.1291597236253756 chrX 155270560 12818741 0.0825574468205692 0.35788220858059766 chrY 59373566 383661 0.006461815010403788 0.12731731406804228