BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975200.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 36,817,004 number of mapped reads = 36,746,682 (99.81%) number of supplementary alignments = 95,599 (0.26%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 18,373,703 number of mapped paired reads (second in pair) = 18,372,979 number of mapped paired reads (both in pair) = 36,701,120 number of mapped paired reads (singletons) = 45,562 number of mapped bases = 3,427,442,968 bp number of sequenced bases = 3,426,256,606 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,758,839 duplication rate = 42.27% >>>>>>> Insert size mean insert size = 105,355.8279 std insert size = 3,125,891.5565 median insert size = 232 >>>>>>> Mapping quality mean mapping quality = 55.7964 >>>>>>> ACTG content number of A's = 934,286,838 bp (27.27%) number of C's = 729,261,076 bp (21.28%) number of T's = 974,476,654 bp (28.44%) number of G's = 787,994,988 bp (23%) number of N's = 237,050 bp (0.01%) GC percentage = 44.28% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 17,819,604 number of insertions = 374,389 mapped reads with insertion percentage = 1% number of deletions = 764,002 mapped reads with deletion percentage = 2.04% homopolymer indels = 46.11% >>>>>>> Coverage mean coverageData = 1.1072X std coverageData = 17.5958X There is a 8.13% of reference with a coverageData >= 1X There is a 4.02% of reference with a coverageData >= 2X There is a 2.64% of reference with a coverageData >= 3X There is a 2.15% of reference with a coverageData >= 4X There is a 1.88% of reference with a coverageData >= 5X There is a 1.72% of reference with a coverageData >= 6X There is a 1.6% of reference with a coverageData >= 7X There is a 1.51% of reference with a coverageData >= 8X There is a 1.43% of reference with a coverageData >= 9X There is a 1.36% of reference with a coverageData >= 10X There is a 1.3% of reference with a coverageData >= 11X There is a 1.24% of reference with a coverageData >= 12X There is a 1.19% of reference with a coverageData >= 13X There is a 1.15% of reference with a coverageData >= 14X There is a 1.11% of reference with a coverageData >= 15X There is a 1.07% of reference with a coverageData >= 16X There is a 1.03% of reference with a coverageData >= 17X There is a 1% of reference with a coverageData >= 18X There is a 0.97% of reference with a coverageData >= 19X There is a 0.94% of reference with a coverageData >= 20X There is a 0.92% of reference with a coverageData >= 21X There is a 0.89% of reference with a coverageData >= 22X There is a 0.87% of reference with a coverageData >= 23X There is a 0.84% of reference with a coverageData >= 24X There is a 0.82% of reference with a coverageData >= 25X There is a 0.8% of reference with a coverageData >= 26X There is a 0.78% of reference with a coverageData >= 27X There is a 0.76% of reference with a coverageData >= 28X There is a 0.75% of reference with a coverageData >= 29X There is a 0.73% of reference with a coverageData >= 30X There is a 0.71% of reference with a coverageData >= 31X There is a 0.7% of reference with a coverageData >= 32X There is a 0.68% of reference with a coverageData >= 33X There is a 0.67% of reference with a coverageData >= 34X There is a 0.65% of reference with a coverageData >= 35X There is a 0.64% of reference with a coverageData >= 36X There is a 0.63% of reference with a coverageData >= 37X There is a 0.61% of reference with a coverageData >= 38X There is a 0.6% of reference with a coverageData >= 39X There is a 0.59% of reference with a coverageData >= 40X There is a 0.58% of reference with a coverageData >= 41X There is a 0.57% of reference with a coverageData >= 42X There is a 0.56% of reference with a coverageData >= 43X There is a 0.55% of reference with a coverageData >= 44X There is a 0.54% of reference with a coverageData >= 45X There is a 0.53% of reference with a coverageData >= 46X There is a 0.52% of reference with a coverageData >= 47X There is a 0.51% of reference with a coverageData >= 48X There is a 0.5% of reference with a coverageData >= 49X There is a 0.49% of reference with a coverageData >= 50X There is a 0.49% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 353353279 1.4176625822729645 19.171221260541515 chr2 243199373 205692195 0.8457760086412722 12.64967990867637 chr3 198022430 198710690 1.0034756668726872 14.956670583480802 chr4 191154276 127762040 0.6683713421090303 12.05745273672383 chr5 180915260 238694365 1.3193710967222998 18.562449249754955 chr6 171115067 228916193 1.337790978979075 19.15653262517283 chr7 159138663 165803694 1.0418819089865043 16.568267204885014 chr8 146364022 103631263 0.7080378195674344 10.791205292789932 chr9 141213431 100841071 0.7141039650824715 11.33349143074907 chr10 135534747 145824156 1.0759171299445447 15.923344734889056 chr11 135006516 195415967 1.447455817614018 18.528266741014434 chr12 133851895 177090632 1.323034178933365 16.88292399296376 chr13 115169878 63651414 0.5526741462728648 13.349031493575584 chr14 107349540 127895907 1.1913968797630619 18.75370530774935 chr15 102531392 84236749 0.8215703245304619 11.304582197346807 chr16 90354753 97967770 1.0842569621102278 14.093708383876798 chr17 81195210 123958696 1.5266749848913501 19.668105256701896 chr18 78077248 62954309 0.8063079912857585 13.692627517126425 chr19 59128983 173599942 2.935953456192541 46.94101816482161 chr20 63025520 60583136 0.9612476977579876 15.601526862545807 chr21 48129895 34429904 0.715353814921059 11.767792198269989 chr22 51304566 40933524 0.7978534308232916 11.512020503943376 chrMT 16571 112869 6.811236497495625 14.530518237325596 chrX 155270560 312514324 2.0127081656690105 29.76200576476398 chrY 59373566 2868879 0.04831912908852401 2.417068330745325