BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695937.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 11,154,700 number of mapped reads = 10,366,013 (92.93%) number of supplementary alignments = 18,643 (0.17%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,254,596 number of mapped paired reads (second in pair) = 5,111,417 number of mapped paired reads (both in pair) = 9,988,310 number of mapped paired reads (singletons) = 377,703 number of mapped bases = 888,140,694 bp number of sequenced bases = 887,838,591 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,093,981 duplication rate = 7.1% >>>>>>> Insert size mean insert size = 44,856.8847 std insert size = 2,023,628.4439 median insert size = 292 >>>>>>> Mapping quality mean mapping quality = 53.2464 >>>>>>> ACTG content number of A's = 225,934,102 bp (25.45%) number of C's = 169,919,606 bp (19.14%) number of T's = 263,729,661 bp (29.7%) number of G's = 227,956,462 bp (25.68%) number of N's = 298,760 bp (0.03%) GC percentage = 44.81% >>>>>>> Mismatches and indels general error rate = 0.0152 number of mismatches = 13,312,750 number of insertions = 87,781 mapped reads with insertion percentage = 0.84% number of deletions = 202,328 mapped reads with deletion percentage = 1.92% homopolymer indels = 42.16% >>>>>>> Coverage mean coverageData = 0.2869X std coverageData = 3.284X There is a 14.66% of reference with a coverageData >= 1X There is a 5.75% of reference with a coverageData >= 2X There is a 2.84% of reference with a coverageData >= 3X There is a 1.58% of reference with a coverageData >= 4X There is a 0.94% of reference with a coverageData >= 5X There is a 0.6% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.27% of reference with a coverageData >= 8X There is a 0.19% of reference with a coverageData >= 9X There is a 0.14% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% 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 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% 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 74957044 0.30072961784115276 2.0328605986914097 chr2 243199373 78520732 0.3228656843617767 6.220497353051079 chr3 198022430 58622880 0.2960416150837054 0.9983602280399168 chr4 191154276 51843764 0.27121425209447053 1.117530206625216 chr5 180915260 52942030 0.29263440795430967 1.3279387233046118 chr6 171115067 52347464 0.30591966515724767 5.244558496145344 chr7 159138663 47830393 0.30055796685937974 2.867648993231481 chr8 146364022 45423937 0.3103490624219113 2.840900813119012 chr9 141213431 39772126 0.28164549022252705 3.849945881924829 chr10 135534747 43193225 0.3186874654364463 1.1426871179076046 chr11 135006516 44860964 0.33228739863192974 6.382775831611149 chr12 133851895 40576583 0.30314537571545025 1.2813317356698013 chr13 115169878 25796439 0.22398598876695866 0.8610419852994752 chr14 107349540 27052507 0.252003939653584 1.6797379400427674 chr15 102531392 26999428 0.26332840580180555 0.9672574019411806 chr16 90354753 29147437 0.32258886259143443 1.8557026739390545 chr17 81195210 26183451 0.3224753159699938 1.7001617249122987 chr18 78077248 24860001 0.31840262863773067 6.786302082393714 chr19 59128983 17591981 0.2975187481239107 1.1616147432547588 chr20 63025520 22033346 0.3495940374629198 1.1514362824605484 chr21 48129895 12227135 0.2540444977077137 2.9104077744004444 chr22 51304566 12122067 0.23627657234250846 0.941458893098425 chrMT 16571 71039 4.286947076217488 11.944565348650745 chrX 155270560 27291005 0.1757641950927465 3.3055089173015664 chrY 59373566 5873716 0.0989281324284952 0.9709502662923271