BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094080.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 = 391,518 number of mapped reads = 354,390 (90.52%) number of supplementary alignments = 11,224 (2.87%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 177,939 number of mapped paired reads (second in pair) = 176,451 number of mapped paired reads (both in pair) = 351,686 number of mapped paired reads (singletons) = 2,704 number of mapped bases = 46,114,092 bp number of sequenced bases = 44,998,614 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 334,952 duplication rate = 49.14% >>>>>>> Insert size mean insert size = 316,219.6569 std insert size = 5,219,403.9305 median insert size = 164 >>>>>>> Mapping quality mean mapping quality = 40.4552 >>>>>>> ACTG content number of A's = 12,111,630 bp (26.92%) number of C's = 10,365,544 bp (23.04%) number of T's = 11,529,930 bp (25.62%) number of G's = 10,990,979 bp (24.43%) number of N's = 531 bp (0%) GC percentage = 47.46% >>>>>>> Mismatches and indels general error rate = 0.0429 number of mismatches = 1,881,499 number of insertions = 28,383 mapped reads with insertion percentage = 7.83% number of deletions = 155,083 mapped reads with deletion percentage = 41.26% homopolymer indels = 28.39% >>>>>>> Coverage mean coverageData = 0.0149X std coverageData = 3.8235X 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% 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 431190 0.0017299455394335808 0.7033714349086856 chr2 243199373 1665253 0.006847275054446789 2.453088394259319 chr3 198022430 1035545 0.005229432847581963 1.6210127752051435 chr4 191154276 567694 0.0029698210883862207 1.1013749448294163 chr5 180915260 520350 0.0028762084525097553 1.33546486457425 chr6 171115067 1070695 0.006257163783245341 2.788790884053091 chr7 159138663 2039669 0.012816929346704389 4.478723353263838 chr8 146364022 800747 0.005470927821319368 1.7132157193337907 chr9 141213431 593335 0.004201689568749307 1.8725230539761586 chr10 135534747 942768 0.006955913674299329 2.5654349336078432 chr11 135006516 1529249 0.011327223643042533 3.2910726528120464 chr12 133851895 886057 0.0066196821494383775 2.0123988145603153 chr13 115169878 1134084 0.00984705393193175 2.9553095007366106 chr14 107349540 284334 0.0026486746007481727 1.051806487152753 chr15 102531392 706645 0.006891986797565374 2.367100785782167 chr16 90354753 396121 0.004384063780241865 1.5583048896758496 chr17 81195210 703743 0.00866729699941659 2.557464085329793 chr18 78077248 112675 0.0014431220731550374 0.36218114755969993 chr19 59128983 201444 0.003406857175270544 1.0214288113224932 chr20 63025520 344457 0.005465357525015264 1.7077244990129496 chr21 48129895 420062 0.008727673309904375 3.4312919488311433 chr22 51304566 106248 0.0020709267865164282 0.48965281116763554 chrMT 16571 864844 52.19021181582282 234.34175678271353 chrX 155270560 28138935 0.18122517881045833 13.772486607052775 chrY 59373566 617948 0.010407796627879821 3.060043510200193