BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006101.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 = 7,918,994 number of mapped reads = 6,884,362 (86.93%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,504,076 number of mapped paired reads (second in pair) = 3,380,286 number of mapped paired reads (both in pair) = 6,221,970 number of mapped paired reads (singletons) = 662,392 number of mapped bases = 265,511,232 bp number of sequenced bases = 265,482,140 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 508,054 duplication rate = 6.71% >>>>>>> Insert size mean insert size = 70,670.6769 std insert size = 2,605,504.4637 median insert size = 101 >>>>>>> Mapping quality mean mapping quality = 46.8018 >>>>>>> ACTG content number of A's = 71,288,282 bp (26.85%) number of C's = 58,126,383 bp (21.89%) number of T's = 73,798,762 bp (27.8%) number of G's = 62,258,717 bp (23.45%) number of N's = 9,996 bp (0%) GC percentage = 45.35% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 1,350,752 number of insertions = 8,784 mapped reads with insertion percentage = 0.13% number of deletions = 23,045 mapped reads with deletion percentage = 0.33% homopolymer indels = 45.2% >>>>>>> Coverage mean coverageData = 0.0858X std coverageData = 0.5243X There is a 4.71% of reference with a coverageData >= 1X There is a 2.07% of reference with a coverageData >= 2X There is a 0.93% of reference with a coverageData >= 3X There is a 0.43% of reference with a coverageData >= 4X There is a 0.2% of reference with a coverageData >= 5X There is a 0.1% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 22771779 0.09136097197527143 0.5736460858173642 chr2 243199373 23089271 0.0949396814439978 0.5571096316630145 chr3 198022430 18181310 0.0918143969852304 0.48717322653613443 chr4 191154276 16053808 0.08398351496986654 0.48215258485458595 chr5 180915260 15993992 0.08840598631646661 0.47906557295722857 chr6 171115067 15186849 0.08875226048913623 0.5557615768003741 chr7 159138663 14663656 0.09214389340445822 0.6273698896144964 chr8 146364022 13434944 0.09179130100701934 0.5599513078589923 chr9 141213431 11303538 0.08004577128361112 0.4796185776910997 chr10 135534747 12830852 0.09466835836569644 0.5118961221683138 chr11 135006516 12449698 0.0922155342487321 0.7314916059570449 chr12 133851895 12141540 0.09070876433986982 0.4878187579749451 chr13 115169878 8163406 0.07088143307749271 0.4317309585291938 chr14 107349540 8239946 0.0767580932344936 0.4545062786463127 chr15 102531392 8194639 0.07992322000270903 0.46238866017765407 chr16 90354753 8543294 0.09455279015593125 0.5261607626879986 chr17 81195210 8154317 0.10042854744756495 0.5547461366981837 chr18 78077248 6897752 0.08834522446282943 0.5545507179961695 chr19 59128983 6024507 0.10188754641695766 0.6064623261817732 chr20 63025520 6218186 0.09866139938234544 0.5184495359888902 chr21 48129895 3506651 0.07285806461867411 0.47061024967840387 chr22 51304566 3780692 0.07369114086258911 0.46541008546361023 chrMT 16571 21715 1.310421821253998 2.1144435348095754 chrX 155270560 7989550 0.051455665517017524 0.37423145403199287 chrY 59373566 1675340 0.02821693411509088 0.2818612760675134