BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006412.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 9,657,332 number of mapped reads = 8,526,090 (88.29%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,299,684 number of mapped paired reads (second in pair) = 4,226,406 number of mapped paired reads (both in pair) = 7,800,062 number of mapped paired reads (singletons) = 726,028 number of mapped bases = 330,156,534 bp number of sequenced bases = 330,116,402 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 369,847 duplication rate = 3.68% >>>>>>> Insert size mean insert size = 76,412.2989 std insert size = 2,596,967.3764 median insert size = 156 >>>>>>> Mapping quality mean mapping quality = 48.2809 >>>>>>> ACTG content number of A's = 92,421,962 bp (28%) number of C's = 70,587,404 bp (21.38%) number of T's = 94,072,692 bp (28.5%) number of G's = 73,020,496 bp (22.12%) number of N's = 13,848 bp (0%) GC percentage = 43.5% >>>>>>> Mismatches and indels general error rate = 0.0034 number of mismatches = 1,112,911 number of insertions = 8,979 mapped reads with insertion percentage = 0.11% number of deletions = 30,133 mapped reads with deletion percentage = 0.35% homopolymer indels = 43.99% >>>>>>> Coverage mean coverageData = 0.1067X std coverageData = 0.6013X There is a 8.69% of reference with a coverageData >= 1X There is a 1.46% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 27435116 0.11007040179049343 0.7893918328455983 chr2 243199373 27428733 0.11278291001186093 0.5158796102295545 chr3 198022430 21787238 0.1100240917152668 0.3855064159348069 chr4 191154276 25565538 0.13374295639612058 0.49178852857503763 chr5 180915260 19221750 0.10624725631215409 0.37762566728886754 chr6 171115067 18184416 0.10627010419836379 0.4191265990207473 chr7 159138663 17363232 0.1091075648913803 0.6000011670404215 chr8 146364022 16909011 0.11552709995903228 1.6141396076011345 chr9 141213431 13716328 0.09713189392020366 0.4335545001651636 chr10 135534747 15274523 0.11269820719848321 0.5986148096735955 chr11 135006516 14706195 0.10892952011294033 0.4725493690336499 chr12 133851895 14568452 0.10884008777014326 0.386766772340428 chr13 115169878 10117496 0.08784845634724038 0.3454412765521816 chr14 107349540 11005613 0.10252128700318604 0.4085746107736663 chr15 102531392 9483403 0.09249267775473097 0.3540247435256686 chr16 90354753 9770685 0.10813692335587481 0.47183391147900433 chr17 81195210 8866826 0.10920380648070249 0.40993537442098693 chr18 78077248 8259886 0.10579120309158438 0.749266562448177 chr19 59128983 6441749 0.1089440181983174 0.5869840541491335 chr20 63025520 7080808 0.11234826781278441 0.412467910185999 chr21 48129895 4156548 0.0863610444194819 0.403338210650234 chr22 51304566 4059338 0.07912235335934817 0.34005045939567513 chrMT 16571 21073 1.271679439985517 1.3745706837180662 chrX 155270560 17936048 0.11551480203330239 0.4360058633754331 chrY 59373566 796529 0.013415549269855208 0.32488208609006247