BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2093997.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 316,352 number of mapped reads = 303,724 (96.01%) number of supplementary alignments = 19,191 (6.07%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 152,700 number of mapped paired reads (second in pair) = 151,024 number of mapped paired reads (both in pair) = 301,068 number of mapped paired reads (singletons) = 2,656 number of mapped bases = 39,095,863 bp number of sequenced bases = 38,399,001 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 284,974 duplication rate = 50.44% >>>>>>> Insert size mean insert size = 1,122,795.0409 std insert size = 9,552,936.967 median insert size = 165 >>>>>>> Mapping quality mean mapping quality = 39.9141 >>>>>>> ACTG content number of A's = 10,106,793 bp (26.32%) number of C's = 9,037,522 bp (23.54%) number of T's = 9,603,905 bp (25.01%) number of G's = 9,650,413 bp (25.13%) number of N's = 368 bp (0%) GC percentage = 48.67% >>>>>>> Mismatches and indels general error rate = 0.0349 number of mismatches = 1,294,316 number of insertions = 20,878 mapped reads with insertion percentage = 6.78% number of deletions = 101,569 mapped reads with deletion percentage = 32.08% homopolymer indels = 29.35% >>>>>>> Coverage mean coverageData = 0.0126X std coverageData = 2.5485X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 0.01% 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 0.01% 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% 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 833685 0.003344765989569992 1.1168723893117098 chr2 243199373 2200285 0.009047247831514763 2.8835362182467907 chr3 198022430 569958 0.002878249701309089 0.7948453016534929 chr4 191154276 1020085 0.005336448764557064 1.9157853635212683 chr5 180915260 381993 0.0021114470940704505 0.9936216149842098 chr6 171115067 899877 0.005258899848953687 1.6809332737078098 chr7 159138663 842799 0.005296004026375413 1.577605190337433 chr8 146364022 485887 0.003319716097990256 1.1303089960260846 chr9 141213431 473627 0.003353979834963432 0.9805391377920252 chr10 135534747 617908 0.004559037543339348 1.457177393515214 chr11 135006516 1020723 0.007560546188748401 1.9269230960035229 chr12 133851895 885780 0.006617612697974878 1.558960416168534 chr13 115169878 869533 0.007550003656337988 2.072578425268924 chr14 107349540 137131 0.0012774251291621742 0.39835836328302926 chr15 102531392 481741 0.004698473224668597 1.4457448465495737 chr16 90354753 289812 0.003207490368547629 0.8539884990426174 chr17 81195210 1217148 0.014990391674582774 3.3686541175103204 chr18 78077248 159209 0.0020391215633010014 0.5684988370952251 chr19 59128983 150661 0.002548005941519407 0.6853549874827475 chr20 63025520 350424 0.005560033459462136 2.0352998960041786 chr21 48129895 89854 0.0018669062128641668 0.37548669048243527 chr22 51304566 139284 0.002714846082120644 0.7051892706382648 chrMT 16571 1094403 66.04326836038864 294.1261288627901 chrX 155270560 23142954 0.1490492080404682 8.296584524163139 chrY 59373566 741102 0.012482019355212723 1.8106227065202538