BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124934.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 4,452,182 number of mapped reads = 4,407,330 (98.99%) number of supplementary alignments = 32,267 (0.72%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,205,895 number of mapped paired reads (second in pair) = 2,201,435 number of mapped paired reads (both in pair) = 4,388,966 number of mapped paired reads (singletons) = 18,364 number of mapped bases = 392,287,042 bp number of sequenced bases = 392,100,378 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 237,392 duplication rate = 3.64% >>>>>>> Insert size mean insert size = 75,206.8964 std insert size = 2,600,292.8504 median insert size = 196 >>>>>>> Mapping quality mean mapping quality = 52.9721 >>>>>>> ACTG content number of A's = 111,884,365 bp (28.53%) number of C's = 74,195,876 bp (18.92%) number of T's = 116,817,278 bp (29.79%) number of G's = 89,197,036 bp (22.75%) number of N's = 5,823 bp (0%) GC percentage = 41.67% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 2,712,519 number of insertions = 45,505 mapped reads with insertion percentage = 1.01% number of deletions = 115,773 mapped reads with deletion percentage = 2.58% homopolymer indels = 47.55% >>>>>>> Coverage mean coverageData = 0.1267X std coverageData = 1.0782X There is a 9.2% of reference with a coverageData >= 1X There is a 2.21% of reference with a coverageData >= 2X There is a 0.53% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 32069931 0.12866540059693574 1.1065902723853118 chr2 243199373 28610140 0.1176406815818559 1.0352809628037194 chr3 198022430 31560485 0.15937833406043952 0.5052945927277859 chr4 191154276 20592240 0.10772576178206968 0.7423388392889053 chr5 180915260 16236050 0.08974394973646778 0.3794876592984758 chr6 171115067 35877448 0.20966855011078597 1.5220629231308882 chr7 159138663 16558929 0.1040534631109726 1.1417856845589414 chr8 146364022 29912941 0.20437359257591323 0.7385042579493764 chr9 141213431 15401165 0.1090630323966847 1.25459226613618 chr10 135534747 20273864 0.14958425384451413 2.7300374152112097 chr11 135006516 19005553 0.14077507933024508 1.2194352556655483 chr12 133851895 17763477 0.13270994034115094 0.4637789716357416 chr13 115169878 13694323 0.11890542247513712 0.4268078781764506 chr14 107349540 9792157 0.09121750312111258 0.40919417933479046 chr15 102531392 9110598 0.08885666937985198 0.37799598820002656 chr16 90354753 8640389 0.09562738774793618 1.0965135241439838 chr17 81195210 10507070 0.12940504741597442 1.5811857909808043 chr18 78077248 10716442 0.1372543509730261 1.4734564363395797 chr19 59128983 6565847 0.1110427859041648 0.7216746232592055 chr20 63025520 10079231 0.159923012138575 0.5410191508519181 chr21 48129895 4626786 0.09613122987282645 0.47706854826350703 chr22 51304566 3393422 0.06614268991184917 0.3354037813757289 chrMT 16571 111668 6.738760485184962 4.792873465643114 chrX 155270560 20360823 0.13113125244090057 0.659680989224746 chrY 59373566 826063 0.013912976020338749 0.7307943184845018