BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081234.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,445,032 number of mapped reads = 2,108,895 (86.25%) number of supplementary alignments = 23,350 (0.95%) number of secondary alignments = 0 number of mapped bases = 137,173,223 bp number of sequenced bases = 137,123,402 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 121,419 duplication rate = 4.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0805 >>>>>>> ACTG content number of A's = 39,010,079 bp (28.45%) number of C's = 26,255,101 bp (19.15%) number of T's = 42,354,045 bp (30.89%) number of G's = 29,486,993 bp (21.5%) number of N's = 17,184 bp (0.01%) GC percentage = 40.65% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 1,255,594 number of insertions = 10,222 mapped reads with insertion percentage = 0.48% number of deletions = 30,720 mapped reads with deletion percentage = 1.44% homopolymer indels = 47.9% >>>>>>> Coverage mean coverageData = 0.0443X std coverageData = 0.3633X There is a 3.4% of reference with a coverageData >= 1X There is a 0.72% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.05% 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 13168699 0.05283316425518555 0.5317710515659966 chr2 243199373 8977337 0.03691348743732164 0.40437525392113216 chr3 198022430 9253619 0.04673015577073769 0.2735214080351947 chr4 191154276 6093020 0.03187488204553687 0.22440004545541617 chr5 180915260 8075598 0.044637461759721095 0.2636956094405006 chr6 171115067 9468690 0.05533522071437461 0.346204377940371 chr7 159138663 9275307 0.05828443462541846 0.6201149209179215 chr8 146364022 8529749 0.058277634649859515 0.4569546350365025 chr9 141213431 3299053 0.02336217579756985 0.2582154351734096 chr10 135534747 4925596 0.036341942631139455 0.32481332215834974 chr11 135006516 8909704 0.06599462206698231 0.45136775611540425 chr12 133851895 4177361 0.03120882972930641 0.22237157315789977 chr13 115169878 3838043 0.03332505917910237 0.23039539983076499 chr14 107349540 4933917 0.04596123094705389 0.273211961902957 chr15 102531392 2597319 0.025331939314741772 0.20471410647534033 chr16 90354753 4549370 0.05035009060342404 0.28943192773028914 chr17 81195210 2212841 0.027253344131999906 0.23276023750481145 chr18 78077248 3311800 0.04241696633569872 0.43514455397516144 chr19 59128983 3561449 0.060231866325182695 0.4600109500693739 chr20 63025520 3464747 0.05497371540925009 0.29642407660146675 chr21 48129895 2536735 0.05270601566864004 0.29601879334148196 chr22 51304566 678951 0.01323373440094981 0.13859901219938967 chrMT 16571 138610 8.364612877919257 6.32353672198522 chrX 155270560 10835987 0.06978777560923333 0.35496626807036 chrY 59373566 359721 0.006058605272251965 0.11262264415064023