BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927007.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 = 25,960,678 number of mapped reads = 25,287,029 (97.41%) number of supplementary alignments = 1,065,206 (4.1%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 12,680,316 number of mapped paired reads (second in pair) = 12,606,713 number of mapped paired reads (both in pair) = 24,858,616 number of mapped paired reads (singletons) = 428,413 number of mapped bases = 2,276,148,410 bp number of sequenced bases = 2,274,356,161 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,407,001 duplication rate = 7.49% >>>>>>> Insert size mean insert size = 472,277.2285 std insert size = 6,726,848.3181 median insert size = 182 >>>>>>> Mapping quality mean mapping quality = 52.2995 >>>>>>> ACTG content number of A's = 652,065,289 bp (28.67%) number of C's = 433,898,156 bp (19.08%) number of T's = 669,621,168 bp (29.44%) number of G's = 518,344,757 bp (22.79%) number of N's = 426,791 bp (0.02%) GC percentage = 41.87% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 21,642,384 number of insertions = 405,602 mapped reads with insertion percentage = 1.57% number of deletions = 1,214,936 mapped reads with deletion percentage = 4.68% homopolymer indels = 51.67% >>>>>>> Coverage mean coverageData = 0.7353X std coverageData = 2.6703X There is a 32.5% of reference with a coverageData >= 1X There is a 16.69% of reference with a coverageData >= 2X There is a 8.97% of reference with a coverageData >= 3X There is a 5.2% of reference with a coverageData >= 4X There is a 3.13% of reference with a coverageData >= 5X There is a 1.96% of reference with a coverageData >= 6X There is a 1.26% of reference with a coverageData >= 7X There is a 0.83% of reference with a coverageData >= 8X There is a 0.56% of reference with a coverageData >= 9X There is a 0.39% of reference with a coverageData >= 10X There is a 0.27% of reference with a coverageData >= 11X There is a 0.2% of reference with a coverageData >= 12X There is a 0.14% of reference with a coverageData >= 13X There is a 0.11% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% 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 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% 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 185825728 0.7455376731037312 3.647176826133393 chr2 243199373 198908887 0.8178840452849359 5.084154643371146 chr3 198022430 158326524 0.7995383351269854 1.5953119915143907 chr4 191154276 139442548 0.7294764779418275 1.9421617580164647 chr5 180915260 137617558 0.7606741299766532 1.56941844161395 chr6 171115067 133733387 0.7815406868876135 2.3834944977368315 chr7 159138663 115956559 0.7286510821069296 1.9114207075863983 chr8 146364022 113774209 0.7773372680343534 1.7809100703618204 chr9 141213431 98803608 0.6996757128576531 3.1827076942653103 chr10 135534747 109071004 0.8047456937371197 3.2418349919070115 chr11 135006516 109236830 0.8091226500504612 2.477476369466856 chr12 133851895 104934595 0.783960473626466 1.6339811510955065 chr13 115169878 69083844 0.5998429901957524 1.3733186672874567 chr14 107349540 69726804 0.6495305336194268 1.5415204791249553 chr15 102531392 66474667 0.648334775363237 1.4855614046570795 chr16 90354753 67075498 0.7423571618861047 3.3507484003387282 chr17 81195210 56058117 0.6904116264986567 1.6411207613861316 chr18 78077248 60879084 0.7797288654436181 3.0074803117676865 chr19 59128983 36621622 0.6193514608563452 2.4057877655942503 chr20 63025520 51703893 0.8203644015947825 1.758535904859807 chr21 48129895 28569135 0.5935839876650468 2.493769008541048 chr22 51304566 26440497 0.5153634278867109 1.4904280274181285 chrMT 16571 1612965 97.3366121537626 81.12488190757912 chrX 155270560 132142405 0.8510461030088382 1.8259463041096204 chrY 59373566 4128442 0.06953333407664954 2.3632837135908322