BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124912.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 = 4,567,640 number of mapped reads = 4,535,660 (99.3%) number of supplementary alignments = 75,117 (1.64%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,272,358 number of mapped paired reads (second in pair) = 2,263,302 number of mapped paired reads (both in pair) = 4,523,544 number of mapped paired reads (singletons) = 12,116 number of mapped bases = 643,302,760 bp number of sequenced bases = 642,806,692 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 687,140 duplication rate = 12.65% >>>>>>> Insert size mean insert size = 55,338.0564 std insert size = 2,253,472.503 median insert size = 180 >>>>>>> Mapping quality mean mapping quality = 53.7455 >>>>>>> ACTG content number of A's = 190,370,713 bp (29.62%) number of C's = 129,274,798 bp (20.11%) number of T's = 189,523,127 bp (29.48%) number of G's = 133,600,110 bp (20.78%) number of N's = 37,944 bp (0.01%) GC percentage = 40.89% >>>>>>> Mismatches and indels general error rate = 0.0118 number of mismatches = 7,292,097 number of insertions = 124,117 mapped reads with insertion percentage = 2.61% number of deletions = 270,171 mapped reads with deletion percentage = 5.73% homopolymer indels = 48.48% >>>>>>> Coverage mean coverageData = 0.2078X std coverageData = 2.763X There is a 10.46% of reference with a coverageData >= 1X There is a 6.05% of reference with a coverageData >= 2X There is a 1.66% of reference with a coverageData >= 3X There is a 0.83% of reference with a coverageData >= 4X There is a 0.3% of reference with a coverageData >= 5X There is a 0.16% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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 0.01% of reference with a coverageData >= 35X There is a 0.01% 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% 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 46309147 0.18579350700995848 3.6883368510667043 chr2 243199373 65241103 0.2682618059216789 2.8880128349903758 chr3 198022430 40841267 0.20624566116070792 0.743019668315483 chr4 191154276 45453327 0.23778346972473688 2.168046759321892 chr5 180915260 42364311 0.2341665982184145 0.7371854111898453 chr6 171115067 32433845 0.18954406276800861 2.4152916042445214 chr7 159138663 32779746 0.2059822885404033 2.3451621590457976 chr8 146364022 32176099 0.21983612202184497 1.1911831706258027 chr9 141213431 36698367 0.25987872924070515 4.696199068039444 chr10 135534747 32154291 0.23724020379807106 6.283872902247897 chr11 135006516 30863570 0.2286080028907642 2.9488906612806978 chr12 133851895 30670517 0.22913771224531412 0.7371222169695573 chr13 115169878 10853288 0.09423721018441993 0.44064344874498756 chr14 107349540 19739621 0.18388174742062238 0.6844227867858085 chr15 102531392 18431048 0.17976004851275207 0.6378997179326968 chr16 90354753 25470329 0.2818925198102196 3.988539598663253 chr17 81195210 14714907 0.18122875721363366 4.824226854505223 chr18 78077248 19418557 0.24870954724223887 3.504677710994443 chr19 59128983 8082224 0.13668802658080556 2.094391263313013 chr20 63025520 13768623 0.21846107735406228 1.0497766639649728 chr21 48129895 8067326 0.16761569914083543 1.2955934649068968 chr22 51304566 5990543 0.1167643246412025 0.5185746320966648 chrMT 16571 99320 5.993603282843522 4.472607884275976 chrX 155270560 29420420 0.18947841754418868 1.298211224096236 chrY 59373566 1260964 0.021237801347488545 1.9245360964859677