BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238333.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,729,116 number of mapped reads = 1,445,425 (83.59%) number of supplementary alignments = 20,774 (1.2%) number of secondary alignments = 0 number of mapped bases = 92,011,772 bp number of sequenced bases = 91,965,408 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,369 duplication rate = 5.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7177 >>>>>>> ACTG content number of A's = 25,980,224 bp (28.25%) number of C's = 17,358,677 bp (18.88%) number of T's = 28,701,914 bp (31.21%) number of G's = 19,904,060 bp (21.64%) number of N's = 20,533 bp (0.02%) GC percentage = 40.52% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 836,555 number of insertions = 7,150 mapped reads with insertion percentage = 0.49% number of deletions = 28,152 mapped reads with deletion percentage = 1.92% homopolymer indels = 45.22% >>>>>>> Coverage mean coverageData = 0.0297X std coverageData = 0.2932X There is a 2.29% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.12% 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% of reference with a coverageData >= 6X There is a 0% 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 8522343 0.0341918626553793 0.46776472531162233 chr2 243199373 5796849 0.023835789247696786 0.31886202488473253 chr3 198022430 5889531 0.029741736832539625 0.2149642383210432 chr4 191154276 5879105 0.03075581212737297 0.2240556653235624 chr5 180915260 10186134 0.056303343344281734 0.30060194572668136 chr6 171115067 6488751 0.03792039540270291 0.30657062795948303 chr7 159138663 5126746 0.032215590500468134 0.4516721432680343 chr8 146364022 3323795 0.022709098551555246 0.32752798033423364 chr9 141213431 2548594 0.01804781586250107 0.2056979041901895 chr10 135534747 4097705 0.03023361234444183 0.26990067633385406 chr11 135006516 5139648 0.03806962917256527 0.2989836253046434 chr12 133851895 5397482 0.040324285285613624 0.252462988208144 chr13 115169878 770002 0.006685793311337883 0.1044571937114945 chr14 107349540 2892004 0.026940068862894056 0.21828909130007765 chr15 102531392 2573589 0.025100498001626663 0.22730371683087708 chr16 90354753 1719221 0.019027455036039996 0.1765320387494241 chr17 81195210 1602006 0.019730301824454916 0.18080063468663593 chr18 78077248 3016520 0.03863507074429672 0.3535861980768113 chr19 59128983 1552144 0.02625013861645481 0.35405907080768484 chr20 63025520 1603156 0.025436616786343055 0.20009886276809866 chr21 48129895 1180639 0.024530263363342054 0.1969200426463263 chr22 51304566 1092364 0.021291750133896465 0.18167423151258769 chrMT 16571 3796 0.2290748898678414 0.5727928211137343 chrX 155270560 5371495 0.034594420217200224 0.2467142230693926 chrY 59373566 238153 0.004011094769008821 0.11761023089537856