BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926992.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 = 37,371,514 number of mapped reads = 36,804,429 (98.48%) number of supplementary alignments = 529,883 (1.42%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 18,469,460 number of mapped paired reads (second in pair) = 18,334,969 number of mapped paired reads (both in pair) = 36,509,690 number of mapped paired reads (singletons) = 294,739 number of mapped bases = 3,514,078,773 bp number of sequenced bases = 3,511,451,761 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,877,088 duplication rate = 6.03% >>>>>>> Insert size mean insert size = 134,260.0647 std insert size = 3,560,595.1069 median insert size = 176 >>>>>>> Mapping quality mean mapping quality = 53.4501 >>>>>>> ACTG content number of A's = 996,862,924 bp (28.39%) number of C's = 720,898,242 bp (20.53%) number of T's = 1,008,429,091 bp (28.72%) number of G's = 784,944,749 bp (22.35%) number of N's = 316,755 bp (0.01%) GC percentage = 42.88% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 32,476,770 number of insertions = 562,832 mapped reads with insertion percentage = 1.5% number of deletions = 1,838,883 mapped reads with deletion percentage = 4.87% homopolymer indels = 52.68% >>>>>>> Coverage mean coverageData = 1.1352X std coverageData = 4.5052X There is a 36.36% of reference with a coverageData >= 1X There is a 22.95% of reference with a coverageData >= 2X There is a 14.8% of reference with a coverageData >= 3X There is a 10.09% of reference with a coverageData >= 4X There is a 7.05% of reference with a coverageData >= 5X There is a 5.04% of reference with a coverageData >= 6X There is a 3.67% of reference with a coverageData >= 7X There is a 2.71% of reference with a coverageData >= 8X There is a 2.02% of reference with a coverageData >= 9X There is a 1.53% of reference with a coverageData >= 10X There is a 1.17% of reference with a coverageData >= 11X There is a 0.9% of reference with a coverageData >= 12X There is a 0.69% of reference with a coverageData >= 13X There is a 0.54% of reference with a coverageData >= 14X There is a 0.42% of reference with a coverageData >= 15X There is a 0.33% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.21% of reference with a coverageData >= 18X There is a 0.17% of reference with a coverageData >= 19X There is a 0.14% of reference with a coverageData >= 20X There is a 0.11% of reference with a coverageData >= 21X There is a 0.09% of reference with a coverageData >= 22X There is a 0.08% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% 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 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 288924319 1.1591719123540318 6.166834250379901 chr2 243199373 304449925 1.2518532479933655 6.8981118313661725 chr3 198022430 234641154 1.1849221020063232 2.3904616462812505 chr4 191154276 209350984 1.095193831813629 3.6232598453851304 chr5 180915260 212988460 1.1772829997867509 2.371295144565338 chr6 171115067 201189385 1.1757549380499615 3.2927723391726214 chr7 159138663 182211467 1.144985533779431 3.1656511227294475 chr8 146364022 182196266 1.2448159288762917 2.9784213376995536 chr9 141213431 150945409 1.0689168015470143 5.872131373444005 chr10 135534747 177691902 1.31104315264631 6.874527139481363 chr11 135006516 171972776 1.2738109322071536 6.360585884051206 chr12 133851895 159869076 1.1943728999877066 2.7800550527227568 chr13 115169878 107348254 0.9320862005254533 2.171503591894764 chr14 107349540 107074576 0.9974386103564113 2.2989685775807756 chr15 102531392 103724133 1.011632934818636 2.3651952632748783 chr16 90354753 115188290 1.274844833010611 6.344717765909092 chr17 81195210 91213282 1.1233825492907772 4.658288859853232 chr18 78077248 86044968 1.102049191078046 5.892387722339252 chr19 59128983 55258386 0.9345397670715899 3.799783929268598 chr20 63025520 77655974 1.2321353953128829 2.763603441360499 chr21 48129895 41441150 0.8610272264254888 3.7782525908104816 chr22 51304566 45493859 0.8867409384186195 2.3733229926191513 chrMT 16571 205729 12.41500211212359 11.150795606118733 chrX 155270560 200892979 1.2938253008168452 3.3212141792185688 chrY 59373566 6106070 0.10284155747020483 3.383073847663047