BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006058.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 = 5,314,664 number of mapped reads = 4,557,294 (85.75%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,327,320 number of mapped paired reads (second in pair) = 2,229,974 number of mapped paired reads (both in pair) = 4,155,692 number of mapped paired reads (singletons) = 401,602 number of mapped bases = 175,816,019 bp number of sequenced bases = 175,796,965 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 260,752 duplication rate = 5.21% >>>>>>> Insert size mean insert size = 79,187.1933 std insert size = 2,808,528.7168 median insert size = 91 >>>>>>> Mapping quality mean mapping quality = 45.6347 >>>>>>> ACTG content number of A's = 45,265,212 bp (25.75%) number of C's = 40,611,305 bp (23.1%) number of T's = 47,012,955 bp (26.74%) number of G's = 42,899,134 bp (24.4%) number of N's = 8,359 bp (0%) GC percentage = 47.5% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 841,434 number of insertions = 5,867 mapped reads with insertion percentage = 0.13% number of deletions = 14,894 mapped reads with deletion percentage = 0.33% homopolymer indels = 43.87% >>>>>>> Coverage mean coverageData = 0.0568X std coverageData = 0.3813X There is a 3.59% of reference with a coverageData >= 1X There is a 1.27% of reference with a coverageData >= 2X There is a 0.46% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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 15167910 0.06085405099151187 0.3941060961299515 chr2 243199373 15360182 0.06315880592340178 0.43861331036756523 chr3 198022430 11614499 0.058652441544122046 0.35331063687789893 chr4 191154276 10670189 0.05581977669178585 0.3546254840920293 chr5 180915260 10401114 0.05749163448124829 0.35203000823778086 chr6 171115067 10128597 0.05919173090701592 0.38480989289523565 chr7 159138663 9475496 0.05954238788596584 0.399067875325931 chr8 146364022 8723601 0.0596020858186037 0.40525931553337635 chr9 141213431 7527766 0.05330771971683062 0.3475411842076017 chr10 135534747 8476293 0.06253963051998762 0.3859255437275273 chr11 135006516 8159758 0.06043973462732717 0.4991862389586088 chr12 133851895 8113003 0.06061179036725629 0.36495762492883443 chr13 115169878 5328622 0.04626749713149822 0.31645142517387903 chr14 107349540 5555648 0.05175288128854581 0.34183930265747225 chr15 102531392 5277486 0.051471904331504635 0.3381508395757556 chr16 90354753 5840851 0.06464353900674157 0.4276151667846364 chr17 81195210 5665126 0.06977167741791665 0.41849093115266167 chr18 78077248 4605113 0.05898149740113791 0.38137957585127796 chr19 59128983 4375285 0.07399560719655875 0.494445129976373 chr20 63025520 4252950 0.06747980817928992 0.402552982578593 chr21 48129895 2405824 0.04998606375517752 0.358810968890343 chr22 51304566 2681845 0.05227302770673472 0.3857634454793501 chrMT 16571 10293 0.6211453744493393 1.2391837323937631 chrX 155270560 4848234 0.031224425287060213 0.25529826879912604 chrY 59373566 1150334 0.01937451424089973 0.23139658292530996