BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695934.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 = 15,433,486 number of mapped reads = 14,228,370 (92.19%) number of supplementary alignments = 241,290 (1.56%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,163,775 number of mapped paired reads (second in pair) = 7,064,595 number of mapped paired reads (both in pair) = 13,910,252 number of mapped paired reads (singletons) = 318,118 number of mapped bases = 1,260,429,976 bp number of sequenced bases = 1,259,987,091 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,813,118 duplication rate = 16.26% >>>>>>> Insert size mean insert size = 498,980.3994 std insert size = 6,888,621.5183 median insert size = 296 >>>>>>> Mapping quality mean mapping quality = 50.5508 >>>>>>> ACTG content number of A's = 341,535,688 bp (27.11%) number of C's = 280,001,920 bp (22.22%) number of T's = 347,188,867 bp (27.55%) number of G's = 290,806,577 bp (23.08%) number of N's = 454,039 bp (0.04%) GC percentage = 45.3% >>>>>>> Mismatches and indels general error rate = 0.0118 number of mismatches = 14,417,062 number of insertions = 149,317 mapped reads with insertion percentage = 1.02% number of deletions = 192,837 mapped reads with deletion percentage = 1.32% homopolymer indels = 40.26% >>>>>>> Coverage mean coverageData = 0.4072X std coverageData = 7.5719X There is a 14.53% of reference with a coverageData >= 1X There is a 7.41% of reference with a coverageData >= 2X There is a 4.55% of reference with a coverageData >= 3X There is a 3.03% of reference with a coverageData >= 4X There is a 2.1% of reference with a coverageData >= 5X There is a 1.48% of reference with a coverageData >= 6X There is a 1.06% of reference with a coverageData >= 7X There is a 0.77% of reference with a coverageData >= 8X There is a 0.57% of reference with a coverageData >= 9X There is a 0.43% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.25% of reference with a coverageData >= 12X There is a 0.19% of reference with a coverageData >= 13X There is a 0.15% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% 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 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% 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 105605813 0.42369327938404616 10.009332468930076 chr2 243199373 102275498 0.4205417832224428 4.235657254794015 chr3 198022430 74887683 0.37817778016359055 1.446126299724699 chr4 191154276 73249953 0.383198087601242 7.99217514977517 chr5 180915260 68228007 0.377126876969914 1.7187831804267253 chr6 171115067 65987603 0.38563292033190744 7.481211553128834 chr7 159138663 64177215 0.4032785860466856 4.378444687790979 chr8 146364022 59225718 0.40464669657684044 2.6894542125022087 chr9 141213431 53317278 0.37756520482814415 5.385060215678094 chr10 135534747 71466386 0.5272919866076852 16.216818648777767 chr11 135006516 58619463 0.43419728718871614 1.8485038961409528 chr12 133851895 53582606 0.40031264406081063 1.9006458821482592 chr13 115169878 31878230 0.27679312120136135 1.1629050721529204 chr14 107349540 36295841 0.3381089569643242 1.405958497466961 chr15 102531392 37011539 0.3609776311239391 1.3346772467202552 chr16 90354753 56084761 0.6207173296129757 14.911046483460385 chr17 81195210 43762002 0.5389727054095925 5.9206524862902015 chr18 78077248 34547307 0.44247598224773493 11.497339929193242 chr19 59128983 31566951 0.5338659553809677 12.931416375806537 chr20 63025520 31027102 0.49229426429167106 3.4579924147760326 chr21 48129895 17147848 0.35628268044216593 3.621150684637862 chr22 51304566 19674471 0.3834838209137175 1.4608608702948884 chrMT 16571 8098473 488.71359604127696 1131.2644653759571 chrX 155270560 35826420 0.23073543368427343 3.452110623013571 chrY 59373566 26885808 0.45282454484879686 11.899222226799495