BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548933.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 = 7,070,153 number of mapped reads = 6,160,803 (87.14%) number of secondary alignments = 0 number of mapped bases = 244,084,627 bp number of sequenced bases = 244,058,272 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 212,125 duplication rate = 2.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.9414 >>>>>>> ACTG content number of A's = 71,798,405 bp (29.42%) number of C's = 50,061,446 bp (20.51%) number of T's = 72,069,191 bp (29.53%) number of G's = 50,127,026 bp (20.54%) number of N's = 2,204 bp (0%) GC percentage = 41.05% >>>>>>> Mismatches and indels general error rate = 0.0026 number of mismatches = 637,346 number of insertions = 7,467 mapped reads with insertion percentage = 0.12% number of deletions = 19,706 mapped reads with deletion percentage = 0.32% homopolymer indels = 41.43% >>>>>>> Coverage mean coverageData = 0.0788X std coverageData = 0.9385X There is a 6.35% of reference with a coverageData >= 1X There is a 1.13% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% 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% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% 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 19079051 0.0765456508130425 0.8287787405458138 chr2 243199373 20628856 0.08482281736803655 0.4474584496832863 chr3 198022430 16751355 0.08459322007107983 0.3467169845581652 chr4 191154276 16208436 0.0847924322655487 0.35624966828792437 chr5 180915260 15292770 0.08453001698143098 0.3507103950807225 chr6 171115067 14372622 0.08399390101632605 0.3773935747951034 chr7 159138663 13565662 0.08524428786988113 0.6851428680875801 chr8 146364022 12919463 0.08826939041071173 3.7464395468538108 chr9 141213431 10260386 0.07265871190396897 0.4358720911789193 chr10 135534747 11133304 0.08214354065234651 0.4191198682671041 chr11 135006516 11160928 0.08266955055710051 0.5227529107733995 chr12 133851895 11089156 0.08284646250245467 0.35192291495371586 chr13 115169878 8019226 0.06962954323872775 0.3125822855325284 chr14 107349540 7542079 0.07025720836810292 0.36285305798073514 chr15 102531392 7024835 0.06851399228053004 0.3104723632657951 chr16 90354753 6650573 0.07360512622949675 0.3431715408107771 chr17 81195210 6101339 0.07514407561726856 0.35459644332630585 chr18 78077248 6616408 0.08474181876902219 0.7574763530450307 chr19 59128983 4394491 0.07432042252443273 0.7377735218361705 chr20 63025520 4913564 0.07796149877065671 0.34490899770176375 chr21 48129895 3053894 0.06345108378067311 0.32853906613072287 chr22 51304566 2610429 0.05088102684661634 0.29371788342000094 chrMT 16571 4923 0.2970852694466236 0.6544778699876816 chrX 155270560 14009510 0.09022644086554463 0.4155915764051299 chrY 59373566 681367 0.011475931898717352 0.1655479066990962