BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046544.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 6,899,882 number of mapped reads = 6,761,763 (98%) number of supplementary alignments = 42,993 (0.62%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,428,513 number of mapped paired reads (second in pair) = 3,333,250 number of mapped paired reads (both in pair) = 6,645,786 number of mapped paired reads (singletons) = 115,977 number of mapped bases = 589,274,068 bp number of sequenced bases = 589,148,647 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,429,844 duplication rate = 45.27% >>>>>>> Insert size mean insert size = 26,532.1543 std insert size = 1,589,926.9514 median insert size = 95 >>>>>>> Mapping quality mean mapping quality = 49.6271 >>>>>>> ACTG content number of A's = 173,166,382 bp (29.39%) number of C's = 122,006,085 bp (20.71%) number of T's = 167,070,291 bp (28.36%) number of G's = 126,853,278 bp (21.53%) number of N's = 52,611 bp (0.01%) GC percentage = 42.24% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 2,293,779 number of insertions = 35,738 mapped reads with insertion percentage = 0.52% number of deletions = 48,799 mapped reads with deletion percentage = 0.71% homopolymer indels = 45.88% >>>>>>> Coverage mean coverageData = 0.1904X std coverageData = 29.1122X There is a 1.56% of reference with a coverageData >= 1X There is a 1.2% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.27% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 183611677 0.736654842677403 80.67168872689537 chr2 243199373 12538849 0.051557900192448276 8.412078655878483 chr3 198022430 18757322 0.0947232189807993 7.836256099725665 chr4 191154276 32243998 0.1686804955385879 22.158127933787792 chr5 180915260 25764285 0.1424107894491598 14.82540560473829 chr6 171115067 28162166 0.1645802821092312 14.488527083008519 chr7 159138663 51384374 0.322890572481434 36.40164559010151 chr8 146364022 64325727 0.4394913867562344 38.67143903873363 chr9 141213431 13554074 0.09598289556465772 11.925865937027348 chr10 135534747 5859715 0.043234042411279226 1.8341489432024132 chr11 135006516 6533503 0.04839398270228675 3.632939774131934 chr12 133851895 6023252 0.044999377857145764 8.359920109478415 chr13 115169878 5240781 0.045504789021309895 3.486682693903958 chr14 107349540 20657419 0.19243136952426623 23.760207375087912 chr15 102531392 11041568 0.10768963323934976 6.7529362495312375 chr16 90354753 54775672 0.6062290049091275 47.5415781135277 chr17 81195210 10900321 0.1342483257325155 9.136615347808162 chr18 78077248 3610266 0.04623966766861455 1.1889148921234292 chr19 59128983 1552716 0.02625981238337889 0.40115785114676966 chr20 63025520 22134948 0.3512061146024658 29.18925271643129 chr21 48129895 3209390 0.06668184088080807 7.873098079521985 chr22 51304566 3617416 0.07050865609115571 10.965812483037928 chrMT 16571 39467 2.381690905799288 2.3320775681025934 chrX 155270560 3430205 0.02209179254586317 1.3311930333094943 chrY 59373566 304957 0.0051362419430896235 1.6180690508391935