BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081958.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,086,366 number of mapped reads = 2,874,016 (93.12%) number of supplementary alignments = 14,106 (0.46%) number of secondary alignments = 0 number of mapped bases = 199,934,366 bp number of sequenced bases = 199,854,997 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 128,451 duplication rate = 3.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4712 >>>>>>> ACTG content number of A's = 58,031,930 bp (29.04%) number of C's = 37,055,434 bp (18.54%) number of T's = 63,469,322 bp (31.76%) number of G's = 41,271,856 bp (20.65%) number of N's = 26,455 bp (0.01%) GC percentage = 39.19% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 1,476,862 number of insertions = 14,443 mapped reads with insertion percentage = 0.5% number of deletions = 44,662 mapped reads with deletion percentage = 1.54% homopolymer indels = 48.64% >>>>>>> Coverage mean coverageData = 0.0646X std coverageData = 0.4796X There is a 5.34% of reference with a coverageData >= 1X There is a 0.83% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% 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 15797116 0.06337844189363123 0.8121538598606463 chr2 243199373 18971801 0.07800925128207464 0.5660306419689787 chr3 198022430 13596613 0.06866198440247401 0.30103302528253884 chr4 191154276 10519619 0.05503208832220944 0.2892363808665847 chr5 180915260 11000957 0.06080723649293045 0.28723650778893245 chr6 171115067 18959913 0.11080212474802116 0.515940042113035 chr7 159138663 13509107 0.08488890597252284 0.5531000951964282 chr8 146364022 11199821 0.07652031453467438 0.829923369132895 chr9 141213431 9712754 0.06878066718738673 0.46628206158086216 chr10 135534747 8302541 0.061257656680467336 0.43993360003203 chr11 135006516 8689763 0.06436550810629021 0.36708862743175047 chr12 133851895 8035041 0.06002934063802384 0.2892248790922913 chr13 115169878 5696138 0.04945857457624467 0.2565004866739737 chr14 107349540 5249078 0.04889707026224798 0.2743844152946519 chr15 102531392 4590290 0.04476960578083247 0.24335763618208642 chr16 90354753 4133633 0.045748927009960395 0.2874155124379626 chr17 81195210 4785165 0.05893407997836326 0.31039442734799033 chr18 78077248 4069441 0.052120702307540345 0.7449967610116087 chr19 59128983 3819505 0.06459615583105835 0.5848760015374713 chr20 63025520 4779465 0.07583380509990238 0.32231266039255135 chr21 48129895 2151796 0.04470809670372229 0.26727968848966066 chr22 51304566 1548069 0.030174097954556327 0.19728934177138624 chrMT 16571 318953 19.24766157745459 11.453289096598693 chrX 155270560 10102117 0.06506138059912968 0.3253338925891952 chrY 59373566 395670 0.00666407673744912 0.1524282341371415