BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124888.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 6,728,386 number of mapped reads = 6,507,445 (96.72%) number of supplementary alignments = 6,137 (0.09%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,269,652 number of mapped paired reads (second in pair) = 3,237,793 number of mapped paired reads (both in pair) = 6,410,664 number of mapped paired reads (singletons) = 96,781 number of mapped bases = 435,437,253 bp number of sequenced bases = 435,268,925 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 429,577 duplication rate = 4.03% >>>>>>> Insert size mean insert size = 36,906.3064 std insert size = 1,814,036.2733 median insert size = 201 >>>>>>> Mapping quality mean mapping quality = 51.7101 >>>>>>> ACTG content number of A's = 123,006,218 bp (28.26%) number of C's = 82,469,427 bp (18.95%) number of T's = 128,014,118 bp (29.41%) number of G's = 101,775,121 bp (23.38%) number of N's = 4,041 bp (0%) GC percentage = 42.33% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 3,002,530 number of insertions = 44,384 mapped reads with insertion percentage = 0.68% number of deletions = 113,226 mapped reads with deletion percentage = 1.72% homopolymer indels = 49.75% >>>>>>> Coverage mean coverageData = 0.1407X std coverageData = 1.4207X There is a 9.94% of reference with a coverageData >= 1X There is a 2.4% of reference with a coverageData >= 2X There is a 0.7% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% 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 0.01% 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 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 41933067 0.16823655977972468 1.7222082835693313 chr2 243199373 37566354 0.15446731435446587 1.2937253795649513 chr3 198022430 26113538 0.13187161676583808 0.5039805562685146 chr4 191154276 18897539 0.09886014268391255 0.6080697304644357 chr5 180915260 20736513 0.1146200326053203 0.4233550590884101 chr6 171115067 30993133 0.18112451196363671 1.069285842472188 chr7 159138663 22064814 0.138651497907834 1.777218350880304 chr8 146364022 21303779 0.14555338606368715 0.6112353832669237 chr9 141213431 16791229 0.1189067419514791 1.1565299645306315 chr10 135534747 21805854 0.16088755453979636 4.274483768496247 chr11 135006516 27714309 0.2052812695351682 0.9747863293244879 chr12 133851895 13942765 0.10416561528695578 0.40986950795233584 chr13 115169878 21065930 0.18291180268507362 0.7669169346612559 chr14 107349540 6750063 0.0628792913318492 0.38964024558066995 chr15 102531392 9109218 0.08884321008730672 0.38526875912981046 chr16 90354753 13672829 0.15132384900659293 2.259294792581324 chr17 81195210 10029965 0.12352902344855073 1.7371898082945936 chr18 78077248 12160816 0.1557536454153712 1.879497165553858 chr19 59128983 6265474 0.1059628236798864 1.098658536089939 chr20 63025520 11429127 0.1813412566845938 0.5680922913237648 chr21 48129895 3597388 0.07474331701741714 0.42492675551092374 chr22 51304566 3130066 0.06100950157145857 0.30580833254952017 chrMT 16571 532653 32.143684750467685 17.23173479767472 chrX 155270560 36915936 0.2377523208520662 0.9346692862842814 chrY 59373566 914894 0.015409113207045707 0.7009654079364426