BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926954.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 8,430,600 number of mapped reads = 8,150,174 (96.67%) number of supplementary alignments = 123,201 (1.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,088,302 number of mapped paired reads (second in pair) = 4,061,872 number of mapped paired reads (both in pair) = 8,022,816 number of mapped paired reads (singletons) = 127,358 number of mapped bases = 747,247,458 bp number of sequenced bases = 746,715,159 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 474,219 duplication rate = 5.08% >>>>>>> Insert size mean insert size = 139,092.034 std insert size = 3,713,393.2672 median insert size = 194 >>>>>>> Mapping quality mean mapping quality = 53.6653 >>>>>>> ACTG content number of A's = 202,519,983 bp (27.12%) number of C's = 155,924,437 bp (20.88%) number of T's = 203,732,636 bp (27.28%) number of G's = 184,498,010 bp (24.71%) number of N's = 40,093 bp (0.01%) GC percentage = 45.59% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 7,387,426 number of insertions = 112,453 mapped reads with insertion percentage = 1.36% number of deletions = 372,325 mapped reads with deletion percentage = 4.46% homopolymer indels = 52.5% >>>>>>> Coverage mean coverageData = 0.2414X std coverageData = 0.9107X There is a 14.31% of reference with a coverageData >= 1X There is a 5.46% of reference with a coverageData >= 2X There is a 2.18% of reference with a coverageData >= 3X There is a 1% of reference with a coverageData >= 4X There is a 0.48% of reference with a coverageData >= 5X There is a 0.25% of reference with a coverageData >= 6X There is a 0.13% 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 0.01% 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 64128102 0.2572836197667889 1.1614131968911128 chr2 243199373 60292409 0.24791350510595273 1.5028280167998973 chr3 198022430 47862213 0.2417009679156043 0.7285153972008278 chr4 191154276 37949077 0.1985259121276471 0.8048524089105357 chr5 180915260 63964465 0.3535603630119427 0.9532670130968204 chr6 171115067 38575396 0.22543541417074628 0.7082098190210637 chr7 159138663 37973866 0.23862124567428344 0.7404878073296166 chr8 146364022 36908224 0.2521673256560277 0.771285200813871 chr9 141213431 26329612 0.18645260449765574 0.7331657669181386 chr10 135534747 37879163 0.2794793500444576 0.8960440603078291 chr11 135006516 37359533 0.2767239249400377 0.8842180917224034 chr12 133851895 33355345 0.2491959116454795 0.8112444417136304 chr13 115169878 20296290 0.1762291525567128 0.617061405939334 chr14 107349540 22789059 0.21228837124034253 0.6980665313858273 chr15 102531392 22966318 0.22399303815167163 0.7195873413065033 chr16 90354753 21845291 0.24177246104585112 0.9031569428814091 chr17 81195210 23315474 0.2871533185270412 0.8336786581171763 chr18 78077248 17797300 0.22794476567616728 0.8443330133137759 chr19 59128983 15622629 0.2642127127402141 0.8993239979942111 chr20 63025520 20425045 0.32407578707799634 0.8780800845868063 chr21 48129895 10071687 0.20926052300758188 1.3425841699293137 chr22 51304566 11577097 0.2256543209039133 0.7355250864246303 chrMT 16571 170374 10.28145555488504 14.978404024894871 chrX 155270560 36703968 0.23638716830801668 0.7222419300283703 chrY 59373566 1089521 0.018350270556429103 0.411039985567879