BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089665.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 21,116,406 number of mapped reads = 16,307,676 (77.23%) number of supplementary alignments = 668 (0%) number of secondary alignments = 0 number of mapped bases = 752,060,308 bp number of sequenced bases = 751,901,000 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,255,869 duplication rate = 6.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.3172 >>>>>>> ACTG content number of A's = 243,046,570 bp (32.32%) number of C's = 152,778,755 bp (20.32%) number of T's = 192,286,371 bp (25.57%) number of G's = 163,605,992 bp (21.76%) number of N's = 183,312 bp (0.02%) GC percentage = 42.08% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 3,731,172 number of insertions = 35,836 mapped reads with insertion percentage = 0.22% number of deletions = 105,580 mapped reads with deletion percentage = 0.65% homopolymer indels = 42.39% >>>>>>> Coverage mean coverageData = 0.2429X std coverageData = 1.2441X There is a 13.99% of reference with a coverageData >= 1X There is a 5.02% of reference with a coverageData >= 2X There is a 2.21% of reference with a coverageData >= 3X There is a 1.11% of reference with a coverageData >= 4X There is a 0.61% of reference with a coverageData >= 5X There is a 0.36% of reference with a coverageData >= 6X There is a 0.22% of reference with a coverageData >= 7X There is a 0.15% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% 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 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% 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 58733771 0.23564142293551196 1.3038125482664238 chr2 243199373 72967475 0.30003150953847235 1.8531925631389217 chr3 198022430 67330223 0.340013113665962 1.0101522565026981 chr4 191154276 34188523 0.17885303805602548 0.7149027199361034 chr5 180915260 31994137 0.1768459830309505 0.6671776741831189 chr6 171115067 49248729 0.2878105935580763 1.0815946204334064 chr7 159138663 51024495 0.32062915471396164 2.036997448603249 chr8 146364022 60629834 0.41424001043097874 2.3826563527808324 chr9 141213431 25171818 0.17825371015877378 1.0345323578229233 chr10 135534747 31304373 0.23096935430144713 1.1240411545851954 chr11 135006516 37047549 0.27441304388597065 1.151717337105959 chr12 133851895 25655889 0.19167370772001396 0.7386486903516833 chr13 115169878 21516447 0.1868235633626355 0.6936029477061086 chr14 107349540 24890798 0.23186683426868898 0.8601252892830813 chr15 102531392 18960865 0.18492741227974355 0.6883423549336234 chr16 90354753 14746994 0.16321215553541493 0.7238685145746306 chr17 81195210 17544492 0.21607791888216066 0.8566478831057606 chr18 78077248 36699616 0.4700423867398605 1.671932523134561 chr19 59128983 12528458 0.21188353603172913 1.3177220331278388 chr20 63025520 17179043 0.27257280860197586 0.8933722076858017 chr21 48129895 11961796 0.24853152079388496 0.9566430142335208 chr22 51304566 6097338 0.11884591324678587 0.5554016885471335 chrMT 16571 223319 13.476495081769356 13.014950336485104 chrX 155270560 22686773 0.14611123319191996 0.8864707780554576 chrY 59373566 1727553 0.029096332196048322 0.51171999262032