BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124829.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 = 28,978,148 number of mapped reads = 28,771,770 (99.29%) number of supplementary alignments = 123,946 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,395,205 number of mapped paired reads (second in pair) = 14,376,565 number of mapped paired reads (both in pair) = 28,690,432 number of mapped paired reads (singletons) = 81,338 number of mapped bases = 2,634,372,949 bp number of sequenced bases = 2,632,952,307 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,767,067 duplication rate = 5.44% >>>>>>> Insert size mean insert size = 76,788.3476 std insert size = 2,646,533.4448 median insert size = 171 >>>>>>> Mapping quality mean mapping quality = 52.9145 >>>>>>> ACTG content number of A's = 760,140,676 bp (28.87%) number of C's = 514,673,794 bp (19.55%) number of T's = 789,216,856 bp (29.97%) number of G's = 568,901,342 bp (21.61%) number of N's = 19,639 bp (0%) GC percentage = 41.15% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 18,739,981 number of insertions = 409,219 mapped reads with insertion percentage = 1.4% number of deletions = 860,191 mapped reads with deletion percentage = 2.93% homopolymer indels = 47.25% >>>>>>> Coverage mean coverageData = 0.851X std coverageData = 9.601X There is a 30.62% of reference with a coverageData >= 1X There is a 18.03% of reference with a coverageData >= 2X There is a 10.76% of reference with a coverageData >= 3X There is a 6.75% of reference with a coverageData >= 4X There is a 4.35% of reference with a coverageData >= 5X There is a 2.88% of reference with a coverageData >= 6X There is a 1.96% of reference with a coverageData >= 7X There is a 1.36% of reference with a coverageData >= 8X There is a 0.97% of reference with a coverageData >= 9X There is a 0.71% of reference with a coverageData >= 10X There is a 0.53% of reference with a coverageData >= 11X There is a 0.4% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.25% of reference with a coverageData >= 14X There is a 0.2% of reference with a coverageData >= 15X There is a 0.17% of reference with a coverageData >= 16X There is a 0.14% of reference with a coverageData >= 17X There is a 0.12% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.09% of reference with a coverageData >= 20X There is a 0.08% 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 0.06% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.03% of reference with a coverageData >= 40X There is a 0.03% 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 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 248160754 0.9956274251368866 15.817139165878157 chr2 243199373 207278587 0.8522990188794607 7.612890517405395 chr3 198022430 180506057 0.9115434903005685 2.484365750981395 chr4 191154276 132452628 0.6929095742540439 3.9068861427373403 chr5 180915260 175303297 0.9689801567872163 1.9243670984074017 chr6 171115067 163813202 0.9573277495195675 6.3289740023348235 chr7 159138663 231700014 1.4559630553135916 14.436519433257248 chr8 146364022 223117859 1.5244037158257375 4.922477694314951 chr9 141213431 106162247 0.7517857632111495 9.737276821584045 chr10 135534747 113602809 0.8381821747894657 28.001034882094793 chr11 135006516 105195719 0.7791899392470805 5.903346778464409 chr12 133851895 66053655 0.4934831516580322 1.3156814233566978 chr13 115169878 122071840 1.0599285344384928 2.3620977998468553 chr14 107349540 55062268 0.5129250483979717 1.840469093758382 chr15 102531392 39250367 0.382813168088072 1.19076655239474 chr16 90354753 46707515 0.516934787038818 6.748042810463615 chr17 81195210 68821134 0.8476009114330759 11.218960435219858 chr18 78077248 71598770 0.9170247650122094 11.988107153759323 chr19 59128983 60545841 1.02396215744147 8.62704195475754 chr20 63025520 65038984 1.031946805040244 2.3797280213580096 chr21 48129895 37686639 0.7830193479541145 2.5509014068110143 chr22 51304566 23270116 0.45356812880943187 1.2958472647556019 chrMT 16571 187685 11.32611188220385 7.445109516498513 chrX 155270560 68662303 0.4422106998261615 2.705977525170436 chrY 59373566 22122659 0.3726011504850492 6.710988996043413