BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617489.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,523,432 (95.39%) number of supplementary alignments = 174,870 (0.55%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,360,029 number of mapped paired reads (second in pair) = 15,163,403 number of mapped paired reads (both in pair) = 30,008,714 number of mapped paired reads (singletons) = 514,718 number of mapped bases = 2,965,376,977 bp number of sequenced bases = 2,963,619,447 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,290,976 duplication rate = 9.98% >>>>>>> Insert size mean insert size = 48,033.1814 std insert size = 2,084,642.1782 median insert size = 221 >>>>>>> Mapping quality mean mapping quality = 52.6668 >>>>>>> ACTG content number of A's = 873,660,686 bp (29.48%) number of C's = 597,674,378 bp (20.17%) number of T's = 873,844,749 bp (29.49%) number of G's = 613,659,311 bp (20.71%) number of N's = 4,780,323 bp (0.16%) GC percentage = 40.87% >>>>>>> Mismatches and indels general error rate = 0.0134 number of mismatches = 38,909,249 number of insertions = 444,093 mapped reads with insertion percentage = 1.43% number of deletions = 1,030,350 mapped reads with deletion percentage = 3.3% homopolymer indels = 47.28% >>>>>>> Coverage mean coverageData = 0.9579X std coverageData = 9.5206X There is a 38.2% of reference with a coverageData >= 1X There is a 20.6% of reference with a coverageData >= 2X There is a 11.62% of reference with a coverageData >= 3X There is a 6.9% of reference with a coverageData >= 4X There is a 4.25% of reference with a coverageData >= 5X There is a 2.72% of reference with a coverageData >= 6X There is a 1.8% of reference with a coverageData >= 7X There is a 1.23% of reference with a coverageData >= 8X There is a 0.86% of reference with a coverageData >= 9X There is a 0.62% of reference with a coverageData >= 10X There is a 0.46% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% 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 0.01% 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 190690234 0.7650541981999716 9.266592654116758 chr2 243199373 306554818 1.2605082579715368 11.23504455430969 chr3 198022430 244799798 1.2362225733721175 2.2424328749594284 chr4 191154276 153138583 0.8011255944910173 5.986228706540918 chr5 180915260 189816419 1.0492007086632713 2.090594265475177 chr6 171115067 139790843 0.816940585366454 5.383084651552533 chr7 159138663 228889084 1.4382996544340705 13.070752644721406 chr8 146364022 131726879 0.899994938646876 3.8115391931376847 chr9 141213431 122946233 0.8706412140074693 17.86853363162713 chr10 135534747 125438895 0.9255109687850009 18.389366592408685 chr11 135006516 167141958 1.2380288222532903 12.310710617915287 chr12 133851895 129901842 0.9704893755893408 2.0528273476681798 chr13 115169878 125737227 1.0917544516284023 2.1674951433575536 chr14 107349540 86133299 0.8023630003444822 2.2367903052768905 chr15 102531392 67114208 0.6545722894311237 1.6380963585147768 chr16 90354753 80154185 0.8871053523880476 14.711724386833028 chr17 81195210 82840879 1.0202680552214842 13.385799269634704 chr18 78077248 52935810 0.6779927745404142 16.58080997703596 chr19 59128983 35531420 0.6009137684644432 5.711539850690764 chr20 63025520 87571528 1.389461411821751 2.7906613869905947 chr21 48129895 42667594 0.8865091851956045 3.713417423279236 chr22 51304566 22187670 0.43246969480260294 1.26400240809685 chrMT 16571 2116521 127.72439804477702 92.1639249303661 chrX 155270560 139411951 0.8978646756989863 4.114127740455831 chrY 59373566 10139099 0.1707678969459237 13.186737606986094