BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549110.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,377,591 number of mapped reads = 8,931,917 (86.07%) number of secondary alignments = 0 number of mapped bases = 354,812,971 bp number of sequenced bases = 354,779,246 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 432,616 duplication rate = 3.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3658 >>>>>>> ACTG content number of A's = 104,955,468 bp (29.58%) number of C's = 72,726,700 bp (20.5%) number of T's = 105,266,879 bp (29.67%) number of G's = 71,828,775 bp (20.25%) number of N's = 1,424 bp (0%) GC percentage = 40.75% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 1,059,493 number of insertions = 8,611 mapped reads with insertion percentage = 0.1% number of deletions = 26,715 mapped reads with deletion percentage = 0.3% homopolymer indels = 45.45% >>>>>>> Coverage mean coverageData = 0.1146X std coverageData = 0.7973X There is a 8.79% of reference with a coverageData >= 1X There is a 1.88% of reference with a coverageData >= 2X There is a 0.43% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% 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 29078037 0.11666184374320977 1.7521980027228363 chr2 243199373 30908264 0.12709022897028605 0.6737523773635823 chr3 198022430 24704583 0.12475648844426361 0.43721264007668076 chr4 191154276 23714761 0.1240608449690134 0.4873982945025058 chr5 180915260 22677426 0.12534833158905445 0.4538762072571075 chr6 171115067 21036940 0.12294031360780171 0.4767294853979191 chr7 159138663 20186922 0.1268511474172684 1.1506120174578869 chr8 146364022 18450899 0.12606171071193986 0.7119926192606812 chr9 141213431 15098003 0.1069161969444677 0.6285886307676647 chr10 135534747 16996687 0.12540464623437117 0.7166518800406699 chr11 135006516 16684063 0.12357968707228917 0.6424312441427874 chr12 133851895 16431805 0.12276109352056615 0.4624804689384814 chr13 115169878 11672178 0.10134748948852755 0.38756214005429185 chr14 107349540 11028301 0.10273263397309387 0.5346828828403049 chr15 102531392 10385380 0.1012897591403031 0.38817118643021387 chr16 90354753 9716908 0.10754174713974372 0.464989785494744 chr17 81195210 8986708 0.11068027288801889 0.458156966761782 chr18 78077248 9786024 0.12533771682116665 1.3553106225445632 chr19 59128983 6441431 0.10893864012509737 1.3314438358693645 chr20 63025520 7344268 0.11652847925729133 0.4687144056545819 chr21 48129895 4668569 0.0969993597534339 0.49071814786137924 chr22 51304566 3784461 0.07376460410950557 0.3548020311277773 chrMT 16571 134990 8.146158952386699 10.737860564416106 chrX 155270560 11652354 0.07504548189946633 0.4588405270110868 chrY 59373566 3243009 0.0546204181167087 0.5997924453713835