BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006017.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 16,982,520 number of mapped reads = 12,211,815 (71.91%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,155,461 number of mapped paired reads (second in pair) = 6,056,354 number of mapped paired reads (both in pair) = 10,805,582 number of mapped paired reads (singletons) = 1,406,233 number of mapped bases = 471,805,186 bp number of sequenced bases = 471,754,549 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 702,310 duplication rate = 5.13% >>>>>>> Insert size mean insert size = 62,748.4713 std insert size = 2,426,919.4287 median insert size = 107 >>>>>>> Mapping quality mean mapping quality = 47.3544 >>>>>>> ACTG content number of A's = 134,865,192 bp (28.59%) number of C's = 99,243,316 bp (21.04%) number of T's = 135,189,456 bp (28.66%) number of G's = 102,093,217 bp (21.64%) number of N's = 363,368 bp (0.08%) GC percentage = 42.68% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 3,139,406 number of insertions = 13,707 mapped reads with insertion percentage = 0.11% number of deletions = 39,673 mapped reads with deletion percentage = 0.32% homopolymer indels = 44.74% >>>>>>> Coverage mean coverageData = 0.1524X std coverageData = 0.6876X There is a 9.8% of reference with a coverageData >= 1X There is a 3.28% of reference with a coverageData >= 2X There is a 1.17% of reference with a coverageData >= 3X There is a 0.47% of reference with a coverageData >= 4X There is a 0.21% of reference with a coverageData >= 5X There is a 0.1% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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% 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 39030921 0.1565930742455402 0.7813729339354778 chr2 243199373 40564353 0.16679464465560115 0.7088888415037383 chr3 198022430 32163442 0.1624232265001495 0.574061040380985 chr4 191154276 30900890 0.1616541918214793 0.6407822712470029 chr5 180915260 29475144 0.16292237592340192 0.5776226448499018 chr6 171115067 27288758 0.1594760676451712 0.6957081304683091 chr7 159138663 25139573 0.1579727548672443 0.7206949490594254 chr8 146364022 23666007 0.16169278950260058 1.2343314470448246 chr9 141213431 19436390 0.1376383950334016 0.6081999501870764 chr10 135534747 21995887 0.16228965255677202 0.7404419994179262 chr11 135006516 21352364 0.15815802549856187 0.6240312818707608 chr12 133851895 21230396 0.15861109773604626 0.5779488300217015 chr13 115169878 15738717 0.1366565396552734 0.5368192795280102 chr14 107349540 14405626 0.13419364442549078 0.5428947815747163 chr15 102531392 13290678 0.12962545168605533 0.5128330991733683 chr16 90354753 13278335 0.14695779202672382 0.609305614342628 chr17 81195210 12284829 0.15129992274174794 0.5743592738384381 chr18 78077248 12694980 0.16259512630363201 0.8401189629254591 chr19 59128983 9000356 0.15221564017091246 0.845713100858248 chr20 63025520 10124017 0.16063361317764613 0.6075163528829834 chr21 48129895 6371975 0.13239120924739187 0.5852966921057887 chr22 51304566 5207127 0.10149441669577713 0.49103066472437334 chrMT 16571 123531 7.4546496892161 6.32818025400698 chrX 155270560 25878865 0.16666948969592174 0.6180220846230258 chrY 59373566 1162025 0.01957142004911748 0.38413108587867395