BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084806.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 = 2,006,846 number of mapped reads = 1,810,592 (90.22%) number of supplementary alignments = 17,670 (0.88%) number of secondary alignments = 0 number of mapped bases = 120,873,709 bp number of sequenced bases = 120,828,084 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 81,246 duplication rate = 3.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3513 >>>>>>> ACTG content number of A's = 32,611,204 bp (26.99%) number of C's = 22,752,561 bp (18.83%) number of T's = 37,792,174 bp (31.28%) number of G's = 27,655,124 bp (22.89%) number of N's = 17,021 bp (0.01%) GC percentage = 41.72% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 901,644 number of insertions = 9,214 mapped reads with insertion percentage = 0.5% number of deletions = 27,563 mapped reads with deletion percentage = 1.51% homopolymer indels = 47.81% >>>>>>> Coverage mean coverageData = 0.039X std coverageData = 0.2699X There is a 3.25% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 8806489 0.035331863827131646 0.2645133593981396 chr2 243199373 10622502 0.043678163594607626 0.4474024321324605 chr3 198022430 9003697 0.0454680664205565 0.25144135221323183 chr4 191154276 6918381 0.036192656239612445 0.22678886646395774 chr5 180915260 7417576 0.041000278251818005 0.23634820978087426 chr6 171115067 6976236 0.040769267851790046 0.24959480154160568 chr7 159138663 7362268 0.04626322642914249 0.30597071090102324 chr8 146364022 5577003 0.038103646810143 0.25518128057217127 chr9 141213431 9188179 0.0650659001409009 0.33604597085778626 chr10 135534747 3529972 0.02604477507159105 0.19886838526954653 chr11 135006516 5373444 0.03980136780953595 0.25249619850520355 chr12 133851895 4967023 0.03710835024039069 0.2248415879973397 chr13 115169878 3216967 0.0279323643982674 0.19451114075042705 chr14 107349540 2409967 0.022449718927533363 0.17494108536939856 chr15 102531392 3238150 0.03158203489522506 0.21585152334154828 chr16 90354753 2185736 0.024190603453921235 0.18788677037062315 chr17 81195210 3161971 0.03894282679975826 0.23467484574930436 chr18 78077248 5105920 0.06539574755503677 0.38938308301575214 chr19 59128983 2290050 0.038729737665198806 0.24964523181623927 chr20 63025520 2285208 0.036258455305089116 0.2236289175548779 chr21 48129895 872822 0.018134716479227722 0.16106867964336774 chr22 51304566 1076543 0.02098337602154163 0.16683829815861517 chrMT 16571 22988 1.3872427735200048 1.5021927450030415 chrX 155270560 9022295 0.05810692638707557 0.2880889087295702 chrY 59373566 242322 0.004081311201688644 0.08315265788481521