BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153390.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 57,684,448 number of mapped reads = 57,292,204 (99.32%) number of supplementary alignments = 448,197 (0.78%) number of secondary alignments = 0 number of mapped bases = 5,562,299,228 bp number of sequenced bases = 5,561,278,526 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,664,069 duplication rate = 31.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.207 >>>>>>> ACTG content number of A's = 1,488,578,854 bp (26.77%) number of C's = 1,285,695,565 bp (23.12%) number of T's = 1,517,475,626 bp (27.29%) number of G's = 1,267,319,419 bp (22.79%) number of N's = 2,209,062 bp (0.04%) GC percentage = 45.91% >>>>>>> Mismatches and indels general error rate = 0.0028 number of mismatches = 14,653,129 number of insertions = 590,924 mapped reads with insertion percentage = 1.02% number of deletions = 479,962 mapped reads with deletion percentage = 0.83% homopolymer indels = 49.79% >>>>>>> Coverage mean coverageData = 1.7968X std coverageData = 16.2492X There is a 25.82% of reference with a coverageData >= 1X There is a 13.51% of reference with a coverageData >= 2X There is a 7.44% of reference with a coverageData >= 3X There is a 5.26% of reference with a coverageData >= 4X There is a 4.04% of reference with a coverageData >= 5X There is a 3.41% of reference with a coverageData >= 6X There is a 3.01% of reference with a coverageData >= 7X There is a 2.73% of reference with a coverageData >= 8X There is a 2.53% of reference with a coverageData >= 9X There is a 2.36% of reference with a coverageData >= 10X There is a 2.23% of reference with a coverageData >= 11X There is a 2.11% of reference with a coverageData >= 12X There is a 2.01% of reference with a coverageData >= 13X There is a 1.92% of reference with a coverageData >= 14X There is a 1.84% of reference with a coverageData >= 15X There is a 1.77% of reference with a coverageData >= 16X There is a 1.7% of reference with a coverageData >= 17X There is a 1.64% of reference with a coverageData >= 18X There is a 1.58% of reference with a coverageData >= 19X There is a 1.52% of reference with a coverageData >= 20X There is a 1.47% of reference with a coverageData >= 21X There is a 1.43% of reference with a coverageData >= 22X There is a 1.38% of reference with a coverageData >= 23X There is a 1.34% of reference with a coverageData >= 24X There is a 1.3% of reference with a coverageData >= 25X There is a 1.26% of reference with a coverageData >= 26X There is a 1.23% of reference with a coverageData >= 27X There is a 1.19% of reference with a coverageData >= 28X There is a 1.16% of reference with a coverageData >= 29X There is a 1.13% of reference with a coverageData >= 30X There is a 1.1% of reference with a coverageData >= 31X There is a 1.07% of reference with a coverageData >= 32X There is a 1.05% of reference with a coverageData >= 33X There is a 1.02% of reference with a coverageData >= 34X There is a 0.99% of reference with a coverageData >= 35X There is a 0.97% of reference with a coverageData >= 36X There is a 0.95% of reference with a coverageData >= 37X There is a 0.93% of reference with a coverageData >= 38X There is a 0.91% of reference with a coverageData >= 39X There is a 0.89% of reference with a coverageData >= 40X There is a 0.87% of reference with a coverageData >= 41X There is a 0.85% of reference with a coverageData >= 42X There is a 0.83% of reference with a coverageData >= 43X There is a 0.81% of reference with a coverageData >= 44X There is a 0.8% of reference with a coverageData >= 45X There is a 0.78% of reference with a coverageData >= 46X There is a 0.76% of reference with a coverageData >= 47X There is a 0.75% of reference with a coverageData >= 48X There is a 0.73% of reference with a coverageData >= 49X There is a 0.72% of reference with a coverageData >= 50X There is a 0.7% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 608387314 2.4408657902601574 21.592613604397425 chr2 243199373 440795390 1.8124857172226345 15.023411494556749 chr3 198022430 332251283 1.677846711607367 13.696895673009621 chr4 191154276 257289632 1.3459789515773113 11.541346319144393 chr5 180915260 246867199 1.3645460255812583 12.742105845657688 chr6 171115067 263878830 1.5421133546352175 13.269485262782386 chr7 159138663 267812789 1.6828895250929687 15.762049606984693 chr8 146364022 215909563 1.4751546182572108 15.544339823618262 chr9 141213431 201704921 1.4283692391837715 14.321771863283377 chr10 135534747 222982268 1.64520370558555 14.173735729531444 chr11 135006516 272395640 2.017648096333365 16.312699992156276 chr12 133851895 309342354 2.3110793762015844 18.552600732560915 chr13 115169878 124043000 1.077043773546413 11.717649942023206 chr14 107349540 180150372 1.6781662222306681 15.22993714935236 chr15 102531392 231293427 2.255830360715282 19.832053533901245 chr16 90354753 218134070 2.4141958530947454 19.774508594862365 chr17 81195210 270268459 3.32862565414881 23.878247119459758 chr18 78077248 111831241 1.4323153526107888 13.316880368024714 chr19 59128983 189277195 3.201089979849645 21.519452181819673 chr20 63025520 114230383 1.8124464978630879 14.329938358576115 chr21 48129895 54411790 1.130519607408244 14.298251661509799 chr22 51304566 80269156 1.5645616415505785 15.097900769769707 chrMT 16571 8809 0.5315913342586446 1.503525355339025 chrX 155270560 344916764 2.2213918981164236 21.4459877461098 chrY 59373566 3847379 0.06479952711615805 2.423088984700761