BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926999.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 38,018,954 number of mapped reads = 37,409,158 (98.4%) number of supplementary alignments = 400,086 (1.05%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 18,765,069 number of mapped paired reads (second in pair) = 18,644,089 number of mapped paired reads (both in pair) = 37,035,456 number of mapped paired reads (singletons) = 373,702 number of mapped bases = 3,532,944,016 bp number of sequenced bases = 3,530,231,545 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,328,830 duplication rate = 7.03% >>>>>>> Insert size mean insert size = 100,445.5885 std insert size = 3,103,194.3841 median insert size = 199 >>>>>>> Mapping quality mean mapping quality = 52.177 >>>>>>> ACTG content number of A's = 1,017,531,911 bp (28.82%) number of C's = 697,753,494 bp (19.77%) number of T's = 1,032,266,603 bp (29.24%) number of G's = 782,287,396 bp (22.16%) number of N's = 392,141 bp (0.01%) GC percentage = 41.92% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 32,111,164 number of insertions = 583,367 mapped reads with insertion percentage = 1.53% number of deletions = 1,919,389 mapped reads with deletion percentage = 4.99% homopolymer indels = 53.12% >>>>>>> Coverage mean coverageData = 1.1412X std coverageData = 4.4217X There is a 36.56% of reference with a coverageData >= 1X There is a 23.04% of reference with a coverageData >= 2X There is a 15.06% of reference with a coverageData >= 3X There is a 10.3% of reference with a coverageData >= 4X There is a 7.21% of reference with a coverageData >= 5X There is a 5.15% of reference with a coverageData >= 6X There is a 3.74% of reference with a coverageData >= 7X There is a 2.75% of reference with a coverageData >= 8X There is a 2.04% of reference with a coverageData >= 9X There is a 1.53% of reference with a coverageData >= 10X There is a 1.15% of reference with a coverageData >= 11X There is a 0.88% of reference with a coverageData >= 12X There is a 0.67% of reference with a coverageData >= 13X There is a 0.52% of reference with a coverageData >= 14X There is a 0.4% of reference with a coverageData >= 15X There is a 0.31% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.19% of reference with a coverageData >= 18X There is a 0.15% of reference with a coverageData >= 19X There is a 0.12% of reference with a coverageData >= 20X There is a 0.1% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% 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 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 301728480 1.2105425406342318 6.1846540686223195 chr2 243199373 327555058 1.346858151644988 7.999621532373653 chr3 198022430 254876723 1.2871103692647343 2.4657582653773256 chr4 191154276 228985745 1.1979106603924465 3.7092938352094205 chr5 180915260 225497165 1.246424237513187 2.3966901744849958 chr6 171115067 217992640 1.273953508722876 3.5755073290789485 chr7 159138663 187155165 1.1760508821165603 3.402300941828365 chr8 146364022 121444206 0.8297408361735236 2.524540909463226 chr9 141213431 163497006 1.1578006769058673 5.993653224933198 chr10 135534747 186104126 1.373110070438247 7.3755612798508166 chr11 135006516 172387216 1.2768807099651398 4.280311172783663 chr12 133851895 157486521 1.1765729652165178 2.4215334008799982 chr13 115169878 113893694 0.9889191165071826 2.154855849012299 chr14 107349540 115347891 1.074507547959684 2.362254983249624 chr15 102531392 109220439 1.0652390147985116 2.3571989549850536 chr16 90354753 4081670 0.045173827214158836 1.8828666719434664 chr17 81195210 88435747 1.0891744352899635 3.153503413291766 chr18 78077248 99698472 1.2769209283605898 5.5409040029317005 chr19 59128983 58217832 0.9845904503380347 3.6409019519001764 chr20 63025520 89119947 1.4140295391454127 2.859153311098496 chr21 48129895 47845050 0.9940817448282403 3.694941759017529 chr22 51304566 43226803 0.8425527466697603 2.157135741724298 chrMT 16571 225562 13.611852030655966 10.964316278842086 chrX 155270560 212820417 1.3706424257116094 3.0603758943914685 chrY 59373566 6100441 0.10274675096995185 3.581317829829282