BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818741.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 3,499,481 number of mapped reads = 3,391,907 (96.93%) number of supplementary alignments = 29,480 (0.84%) number of secondary alignments = 0 number of mapped bases = 230,402,272 bp number of sequenced bases = 230,306,914 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,947,953 duplication rate = 47.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.8328 >>>>>>> ACTG content number of A's = 63,461,497 bp (27.56%) number of C's = 50,158,072 bp (21.78%) number of T's = 69,020,521 bp (29.97%) number of G's = 47,652,003 bp (20.69%) number of N's = 14,821 bp (0.01%) GC percentage = 42.47% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 1,195,017 number of insertions = 29,466 mapped reads with insertion percentage = 0.86% number of deletions = 59,777 mapped reads with deletion percentage = 1.74% homopolymer indels = 39.11% >>>>>>> Coverage mean coverageData = 0.0744X std coverageData = 0.8555X There is a 2.57% of reference with a coverageData >= 1X There is a 1.5% of reference with a coverageData >= 2X There is a 1.01% of reference with a coverageData >= 3X There is a 0.7% of reference with a coverageData >= 4X There is a 0.48% of reference with a coverageData >= 5X There is a 0.33% of reference with a coverageData >= 6X There is a 0.23% of reference with a coverageData >= 7X There is a 0.15% of reference with a coverageData >= 8X There is a 0.11% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% 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% 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 18990117 0.07618884528275659 1.1989361738235456 chr2 243199373 20358109 0.08370954558340905 1.4134108925587507 chr3 198022430 15703556 0.07930190534476322 0.6266313921397497 chr4 191154276 15222754 0.07963595854899945 0.7249410491463858 chr5 180915260 14417650 0.07969283519809219 0.6682951317052314 chr6 171115067 13648483 0.07976201768369118 0.692823171906916 chr7 159138663 12599981 0.0791761144807406 0.774959332743288 chr8 146364022 11820506 0.08076100833031222 0.740361000756 chr9 141213431 9958091 0.07051801609437561 0.714141919070343 chr10 135534747 10892201 0.08036463889219493 0.8953387802470806 chr11 135006516 10852540 0.08038530525445158 0.7062321611454411 chr12 133851895 10507570 0.07850146611671056 0.656176368680937 chr13 115169878 7567878 0.06571056713284007 0.5822291426463265 chr14 107349540 7152449 0.06662766323917177 0.6445391079022231 chr15 102531392 6540274 0.06378801528413854 0.566840126202795 chr16 90354753 6780903 0.07504755173200463 0.924037250982267 chr17 81195210 6090747 0.07501362457218844 0.6567317044922717 chr18 78077248 6333869 0.08112310772019014 1.0570903240839864 chr19 59128983 4428594 0.07489717859683127 1.002165528923279 chr20 63025520 4987116 0.07912851809870033 0.6829127606026941 chr21 48129895 3212286 0.06674201138398494 0.6227971665841361 chr22 51304566 2720361 0.05302376010743371 0.5794215425693438 chrMT 16571 295192 17.81377104580291 15.083007148767592 chrX 155270560 7123389 0.04587726739698755 0.5548467599603144 chrY 59373566 2197656 0.03701404763190407 1.3048913467549144