BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549102.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,687,610 number of mapped reads = 9,111,926 (85.26%) number of secondary alignments = 0 number of mapped bases = 361,549,668 bp number of sequenced bases = 361,516,361 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 421,564 duplication rate = 3.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1436 >>>>>>> ACTG content number of A's = 109,034,417 bp (30.16%) number of C's = 71,175,503 bp (19.69%) number of T's = 110,102,692 bp (30.46%) number of G's = 71,202,307 bp (19.7%) number of N's = 1,442 bp (0%) GC percentage = 39.38% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 1,079,455 number of insertions = 9,113 mapped reads with insertion percentage = 0.1% number of deletions = 26,615 mapped reads with deletion percentage = 0.29% homopolymer indels = 45.33% >>>>>>> Coverage mean coverageData = 0.1168X std coverageData = 0.8339X There is a 9.13% of reference with a coverageData >= 1X There is a 1.8% of reference with a coverageData >= 2X There is a 0.4% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% 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 28165794 0.11300190100629678 1.662474229020263 chr2 243199373 31668620 0.13021670084651082 0.6857834693145372 chr3 198022430 26184866 0.1322318183854223 0.4450788501185699 chr4 191154276 25817745 0.13506234618575835 0.4672266194487687 chr5 180915260 24395314 0.1348438711029683 0.46029798095900315 chr6 171115067 22359254 0.13066794404492738 0.5150506211128578 chr7 159138663 20628299 0.12962468460602813 1.1350536960181972 chr8 146364022 19663749 0.13434824167376325 1.533396310733855 chr9 141213431 15335615 0.10859884142323545 0.6560625312108056 chr10 135534747 17039740 0.12572229909426844 0.6718183831881818 chr11 135006516 16432872 0.12171910280241585 0.6393506314973199 chr12 133851895 16617440 0.12414796219358717 0.4593503452182196 chr13 115169878 13620524 0.11826463860628558 0.41434620056826227 chr14 107349540 11294227 0.10520983136024617 0.5342608739655164 chr15 102531392 10000389 0.0975348993603832 0.3742301472669916 chr16 90354753 8970912 0.09928544655531292 0.45638066314541864 chr17 81195210 7827944 0.09640893840905147 0.42639931886000754 chr18 78077248 10078806 0.12908761845704397 1.4277622530232537 chr19 59128983 5171553 0.08746223489079796 1.2867883689987432 chr20 63025520 6794359 0.10780329936190927 0.4329254181584265 chr21 48129895 4800527 0.09974106529839719 0.46636356440165194 chr22 51304566 3020425 0.058872440320419044 0.3136128851744923 chrMT 16571 87692 5.291895480055518 6.501768850531157 chrX 155270560 12491664 0.08045094961981203 0.4639247903535111 chrY 59373566 3081338 0.05189747235326913 0.4467176875819502