BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053631.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 = 11,905,178 number of mapped reads = 9,384,536 (78.83%) number of supplementary alignments = 270 (0%) number of secondary alignments = 0 number of mapped bases = 444,594,782 bp number of sequenced bases = 444,513,975 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,237,164 duplication rate = 16.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5129 >>>>>>> ACTG content number of A's = 130,179,147 bp (29.29%) number of C's = 85,977,244 bp (19.34%) number of T's = 130,466,825 bp (29.35%) number of G's = 97,882,402 bp (22.02%) number of N's = 8,357 bp (0%) GC percentage = 41.36% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 2,429,836 number of insertions = 16,971 mapped reads with insertion percentage = 0.18% number of deletions = 54,290 mapped reads with deletion percentage = 0.58% homopolymer indels = 46.98% >>>>>>> Coverage mean coverageData = 0.1436X std coverageData = 1.0418X There is a 5.83% of reference with a coverageData >= 1X There is a 2.62% of reference with a coverageData >= 2X There is a 1.55% of reference with a coverageData >= 3X There is a 1.01% of reference with a coverageData >= 4X There is a 0.7% of reference with a coverageData >= 5X There is a 0.51% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.29% of reference with a coverageData >= 8X There is a 0.23% of reference with a coverageData >= 9X There is a 0.18% of reference with a coverageData >= 10X There is a 0.15% of reference with a coverageData >= 11X There is a 0.12% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% 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 0.02% 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 0.01% 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% 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 36001367 0.14443842448841882 1.0859091949340929 chr2 243199373 36803520 0.1513306533072353 1.1987297944690036 chr3 198022430 30308117 0.15305395959437523 1.0456386125102957 chr4 191154276 27772484 0.14528832198344335 1.0186552262400819 chr5 180915260 27862463 0.15400836281030136 0.9911945265607441 chr6 171115067 26177872 0.15298402682447595 1.0290552192107933 chr7 159138663 22959677 0.14427466315963708 1.1356611889875354 chr8 146364022 22915926 0.15656802598660483 1.0634340727384708 chr9 141213431 18608950 0.13177889573407503 1.013845406621852 chr10 135534747 20411513 0.15059985318746344 1.0906685180227156 chr11 135006516 20073837 0.14868791221899244 1.0785750273387231 chr12 133851895 20559500 0.1535988713495614 1.0149804957614292 chr13 115169878 14879937 0.12919990242587562 0.9324004899802056 chr14 107349540 13625905 0.12693025978499767 1.0502167607889896 chr15 102531392 13087859 0.1276473355594353 0.8882953399180862 chr16 90354753 12881145 0.14256189710352038 0.9871542517547729 chr17 81195210 11778201 0.14506029358135783 0.9558844889101803 chr18 78077248 11711204 0.14999509204012929 1.0868103357741752 chr19 59128983 8069974 0.13648085237657478 1.0293995989994822 chr20 63025520 9639679 0.15294882136632906 1.0297276144846674 chr21 48129895 5629513 0.1169649964954214 0.955719529929352 chr22 51304566 5027304 0.0979894070247081 0.7822646578709493 chrMT 16571 33320 2.0107416571118217 3.950359468491694 chrX 155270560 26589731 0.17124773041328634 1.1336266848419723 chrY 59373566 1185784 0.019971581292590714 0.42036587807775516