BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006042.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 = 13,783,358 number of mapped reads = 12,211,637 (88.6%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,200,619 number of mapped paired reads (second in pair) = 6,011,018 number of mapped paired reads (both in pair) = 11,297,074 number of mapped paired reads (singletons) = 914,563 number of mapped bases = 472,297,414 bp number of sequenced bases = 472,249,289 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 883,560 duplication rate = 6.44% >>>>>>> Insert size mean insert size = 52,706.1448 std insert size = 2,238,331.6923 median insert size = 92 >>>>>>> Mapping quality mean mapping quality = 47.1153 >>>>>>> ACTG content number of A's = 130,106,409 bp (27.55%) number of C's = 103,126,764 bp (21.84%) number of T's = 133,075,528 bp (28.18%) number of G's = 105,749,593 bp (22.39%) number of N's = 190,995 bp (0.04%) GC percentage = 44.23% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 2,681,014 number of insertions = 13,720 mapped reads with insertion percentage = 0.11% number of deletions = 38,113 mapped reads with deletion percentage = 0.31% homopolymer indels = 46.61% >>>>>>> Coverage mean coverageData = 0.1526X std coverageData = 0.8069X There is a 7.86% of reference with a coverageData >= 1X There is a 3.72% of reference with a coverageData >= 2X There is a 1.75% of reference with a coverageData >= 3X There is a 0.86% of reference with a coverageData >= 4X There is a 0.44% of reference with a coverageData >= 5X There is a 0.23% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 39566143 0.15874039888550567 0.8646013370683203 chr2 243199373 41398736 0.17022550465210287 0.8646758504938156 chr3 198022430 33053347 0.1669171871085513 0.6836275457928722 chr4 191154276 29441712 0.15402068222632906 0.6879830387349591 chr5 180915260 28711234 0.1586999018214384 0.6668460243697654 chr6 171115067 27260405 0.1593103721252086 0.7733455250485881 chr7 159138663 25938823 0.1629951044643375 1.1107560663209572 chr8 146364022 24032413 0.16419617793777216 0.9525733020411982 chr9 141213431 20300661 0.14375871229982365 0.752764657685621 chr10 135534747 22624033 0.16692422792510914 0.7233127767979485 chr11 135006516 22179323 0.16428335207168815 1.2936657022635345 chr12 133851895 21980875 0.16421788425184417 0.6847253846014959 chr13 115169878 14970858 0.1299893536398467 0.6066643131873471 chr14 107349540 14785998 0.1377369479179883 0.6514071248471998 chr15 102531392 14134506 0.13785539944683478 0.6325688782914878 chr16 90354753 14539288 0.16091337220522312 0.7352977663697803 chr17 81195210 13461762 0.1657950265785383 0.8200224160974801 chr18 78077248 12564225 0.1609204386916916 1.0873746774513442 chr19 59128983 9851514 0.1666105774219049 0.9064232488723517 chr20 63025520 11033550 0.17506479914802767 0.7222263529031335 chr21 48129895 6428697 0.1335697283362035 0.7015353612498333 chr22 51304566 6183400 0.12052338577427982 0.6501940383257299 chrMT 16571 60486 3.650111640818297 4.5923597594740295 chrX 155270560 14708252 0.09472659852582485 0.5595887541299723 chrY 59373566 3087173 0.05199574841100162 0.4236858749781353