BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819128.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 = 1,919,642 number of mapped reads = 1,754,490 (91.4%) number of supplementary alignments = 7,013 (0.37%) number of secondary alignments = 0 number of mapped bases = 103,052,760 bp number of sequenced bases = 103,019,856 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 105,049 duplication rate = 4.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3899 >>>>>>> ACTG content number of A's = 26,423,332 bp (25.65%) number of C's = 19,478,696 bp (18.91%) number of T's = 32,931,715 bp (31.97%) number of G's = 24,184,710 bp (23.48%) number of N's = 1,403 bp (0%) GC percentage = 42.38% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 528,266 number of insertions = 7,259 mapped reads with insertion percentage = 0.41% number of deletions = 19,523 mapped reads with deletion percentage = 1.1% homopolymer indels = 42.33% >>>>>>> Coverage mean coverageData = 0.0333X std coverageData = 0.3181X There is a 2.84% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% 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 10217775 0.04099398011128726 0.6001556770335704 chr2 243199373 8074614 0.033201623426882765 0.3710460185561538 chr3 198022430 5586706 0.028212490877927314 0.19235151213884763 chr4 191154276 5743314 0.03004543827206879 0.25585049161778617 chr5 180915260 5682216 0.031408163136708314 0.20242189774239655 chr6 171115067 4410984 0.025777881967576823 0.23307861798095494 chr7 159138663 5090530 0.031988015382534665 0.36468509829191925 chr8 146364022 9368689 0.06400950774637773 0.3699748188487948 chr9 141213431 4392026 0.031102041561471585 0.26634378232987577 chr10 135534747 5468302 0.04034612614874324 0.3465585198022669 chr11 135006516 3539224 0.02621520875333158 0.2719329539282143 chr12 133851895 4754924 0.03552377050769434 0.21544300481872586 chr13 115169878 2257336 0.019600055493676913 0.1600575061047839 chr14 107349540 2388571 0.02225040740742811 0.17619075325889808 chr15 102531392 2745026 0.02677254201327921 0.18699809809421122 chr16 90354753 3194268 0.03535251764785412 0.23090106640950875 chr17 81195210 3641663 0.04485071225260702 0.2587400099795602 chr18 78077248 2461864 0.03153113183497451 0.485941958873187 chr19 59128983 2118733 0.035832393734896474 0.3933531336944204 chr20 63025520 3006410 0.04770147076930107 0.25471396180130706 chr21 48129895 1417505 0.029451653696730484 0.23654358536030157 chr22 51304566 855373 0.01667245367595547 0.14532207352688198 chrMT 16571 104527 6.3078269265584455 4.570024535307018 chrX 155270560 6135139 0.039512570831199426 0.2500156152458024 chrY 59373566 397041 0.006687167821451048 0.2316166824754234