BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054610.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 15,778,203 number of mapped reads = 11,617,588 (73.63%) number of supplementary alignments = 318 (0%) number of secondary alignments = 0 number of mapped bases = 548,037,902 bp number of sequenced bases = 547,928,841 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,012,756 duplication rate = 18.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4025 >>>>>>> ACTG content number of A's = 165,176,619 bp (30.15%) number of C's = 103,537,232 bp (18.9%) number of T's = 166,007,490 bp (30.3%) number of G's = 113,205,008 bp (20.66%) number of N's = 2,492 bp (0%) GC percentage = 39.56% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 3,057,752 number of insertions = 22,221 mapped reads with insertion percentage = 0.19% number of deletions = 73,905 mapped reads with deletion percentage = 0.63% homopolymer indels = 47.46% >>>>>>> Coverage mean coverageData = 0.177X std coverageData = 1.2946X There is a 6.92% of reference with a coverageData >= 1X There is a 3.14% of reference with a coverageData >= 2X There is a 1.83% of reference with a coverageData >= 3X There is a 1.2% of reference with a coverageData >= 4X There is a 0.84% of reference with a coverageData >= 5X There is a 0.62% of reference with a coverageData >= 6X There is a 0.47% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.3% of reference with a coverageData >= 9X There is a 0.24% of reference with a coverageData >= 10X There is a 0.2% of reference with a coverageData >= 11X There is a 0.17% of reference with a coverageData >= 12X There is a 0.14% of reference with a coverageData >= 13X There is a 0.12% of reference with a coverageData >= 14X There is a 0.11% of reference with a coverageData >= 15X There is a 0.09% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% 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 48774834 0.1956859076391228 1.40534208262295 chr2 243199373 46820445 0.19251877347562077 1.4913756496271229 chr3 198022430 39746400 0.2007166561888974 1.2836692509294891 chr4 191154276 33951900 0.17761517403879576 1.224780173045849 chr5 180915260 27582810 0.15246259491874814 1.032749431207003 chr6 171115067 27694435 0.16184685244578725 1.2239533723443008 chr7 159138663 32402536 0.20361196574838636 1.5294479542934578 chr8 146364022 29138529 0.199082592851951 1.380609117182949 chr9 141213431 27289842 0.19325245344403535 1.4158596845498603 chr10 135534747 22720557 0.1676363995426206 1.242038091360495 chr11 135006516 24821297 0.1838525853078084 1.323152819198565 chr12 133851895 20043951 0.14974723368690446 1.0424108692521539 chr13 115169878 18177481 0.1578319028869684 1.0741861409687818 chr14 107349540 12832938 0.11954348383793727 1.062121210791981 chr15 102531392 14162919 0.13813251457660888 0.9771687982619649 chr16 90354753 14840644 0.16424862563677198 1.2853783079136065 chr17 81195210 10029193 0.12351951549851278 0.9069280875632009 chr18 78077248 20924074 0.2679919507408868 1.795208670857786 chr19 59128983 9664714 0.16345138220963482 1.2868658676023825 chr20 63025520 8215995 0.1303598129773463 1.030870203852932 chr21 48129895 6982289 0.14507176880398348 1.2308185222734722 chr22 51304566 6509977 0.12688884260321 0.9491170572744376 chrMT 16571 33174 2.001931084424597 3.9338101123718525 chrX 155270560 43106411 0.2776212760487242 1.679827373984464 chrY 59373566 1570557 0.026452125176378998 0.5800940065252136