BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084401.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 = 2,895,048 number of mapped reads = 2,650,022 (91.54%) number of supplementary alignments = 19,907 (0.69%) number of secondary alignments = 0 number of mapped bases = 178,149,482 bp number of sequenced bases = 178,087,550 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 99,107 duplication rate = 3.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1764 >>>>>>> ACTG content number of A's = 50,926,852 bp (28.6%) number of C's = 33,701,607 bp (18.92%) number of T's = 55,338,920 bp (31.07%) number of G's = 37,896,583 bp (21.28%) number of N's = 223,588 bp (0.13%) GC percentage = 40.2% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 1,767,730 number of insertions = 12,821 mapped reads with insertion percentage = 0.48% number of deletions = 36,014 mapped reads with deletion percentage = 1.35% homopolymer indels = 46.68% >>>>>>> Coverage mean coverageData = 0.0575X std coverageData = 0.384X There is a 4.77% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.14% 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 17307184 0.06943687414122832 0.6486663771527685 chr2 243199373 17015732 0.06996618367104096 0.4278856074613963 chr3 198022430 11843386 0.05980830555407284 0.29022637453060224 chr4 191154276 9023550 0.0472055880141546 0.26071340931933545 chr5 180915260 8989194 0.049687317697799514 0.25937135693825636 chr6 171115067 8699187 0.05083822922501617 0.2956947477635659 chr7 159138663 10180545 0.06397279459360546 0.5251556264405859 chr8 146364022 8973118 0.06130685586106673 0.3934706649987908 chr9 141213431 6907252 0.048913562619974864 0.32859786937581914 chr10 135534747 11633554 0.08583447608457188 0.5473387989141625 chr11 135006516 9933184 0.07357558949228792 0.3808592315486486 chr12 133851895 9176358 0.06855605593032509 0.3057723216345899 chr13 115169878 4534682 0.03937385433368263 0.2305291946927873 chr14 107349540 4769951 0.04443382803503396 0.25480722475678086 chr15 102531392 3831537 0.03736940389924678 0.23007244749513536 chr16 90354753 3755475 0.04156366848792116 0.25671769271553563 chr17 81195210 4859834 0.059853703192589806 0.30775190846840367 chr18 78077248 4832467 0.06189340843570716 0.5161851713040954 chr19 59128983 3470050 0.05868610999110199 0.4775028933748959 chr20 63025520 3522899 0.05589638927215515 0.2771893647367227 chr21 48129895 1650660 0.034295940184369815 0.22631852290881052 chr22 51304566 1390414 0.027101174581615213 0.18794451845309001 chrMT 16571 42916 2.5898255989379035 2.0828660369451875 chrX 155270560 11457888 0.07379304872733118 0.3466203189882459 chrY 59373566 348465 0.005869025956770055 0.1114622535967817