BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695984.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 10,898,304 number of mapped reads = 9,577,964 (87.88%) number of supplementary alignments = 24,541 (0.23%) number of secondary alignments = 0 number of mapped bases = 1,248,504,216 bp number of sequenced bases = 1,238,718,130 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,824,954 duplication rate = 16.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.9645 >>>>>>> ACTG content number of A's = 348,679,897 bp (28.15%) number of C's = 267,701,143 bp (21.61%) number of T's = 342,995,861 bp (27.69%) number of G's = 279,341,229 bp (22.55%) number of N's = 0 bp (0%) GC percentage = 44.16% >>>>>>> Mismatches and indels general error rate = 0.021 number of mismatches = 18,400,493 number of insertions = 6,969,898 mapped reads with insertion percentage = 45.2% number of deletions = 8,783,284 mapped reads with deletion percentage = 53.08% homopolymer indels = 37.48% >>>>>>> Coverage mean coverageData = 0.4033X std coverageData = 1.4311X There is a 16.51% of reference with a coverageData >= 1X There is a 8.56% of reference with a coverageData >= 2X There is a 4.86% of reference with a coverageData >= 3X There is a 2.98% of reference with a coverageData >= 4X There is a 1.93% of reference with a coverageData >= 5X There is a 1.31% of reference with a coverageData >= 6X There is a 0.92% of reference with a coverageData >= 7X There is a 0.66% of reference with a coverageData >= 8X There is a 0.49% of reference with a coverageData >= 9X There is a 0.36% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.21% of reference with a coverageData >= 12X There is a 0.16% of reference with a coverageData >= 13X There is a 0.13% of reference with a coverageData >= 14X There is a 0.1% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 114148266 0.4579658238845471 1.596211564440287 chr2 243199373 105937697 0.43560020609099187 1.6484825172118647 chr3 198022430 81923568 0.4137085278672724 1.327556743047889 chr4 191154276 61103559 0.31965572666551284 1.2709753859181876 chr5 180915260 71776445 0.3967406895360845 1.2915462513186395 chr6 171115067 67236871 0.3929336684302616 1.283130381964296 chr7 159138663 61805910 0.388377713089119 1.2853539637574152 chr8 146364022 62202965 0.4249880821121464 1.3806826148883273 chr9 141213431 68404936 0.4844081438684115 1.642037397482203 chr10 135534747 63738381 0.4702733609706742 1.5175916758141286 chr11 135006516 65017201 0.4815856517621712 1.531404838860197 chr12 133851895 57281751 0.42794874887651013 1.3953276579064813 chr13 115169878 33720754 0.29279143631636045 1.1101715749259753 chr14 107349540 37831405 0.35241329399268967 1.225632143138827 chr15 102531392 40911239 0.3990118362969265 1.3396827729237777 chr16 90354753 44289772 0.49017644926769927 2.008404855363653 chr17 81195210 40263934 0.4958905088120346 1.5441126902674907 chr18 78077248 32765081 0.4196495373402505 1.463655410478838 chr19 59128983 24415988 0.4129275824006647 1.4018358293542406 chr20 63025520 36903762 0.5855368111203207 1.6943010843572734 chr21 48129895 15422342 0.3204316568735502 1.9720449928942323 chr22 51304566 20779901 0.4050302462357834 1.3900264947502796 chrMT 16571 437631 26.409450244402873 25.48038833870462 chrX 155270560 34039084 0.2192243268781925 0.8495520365654389 chrY 59373566 6145773 0.1035102557255867 0.8256399355509565