BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038432.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 14,577,296 number of mapped reads = 13,857,489 (95.06%) number of supplementary alignments = 216,768 (1.49%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,021,391 number of mapped paired reads (second in pair) = 6,836,098 number of mapped paired reads (both in pair) = 13,635,988 number of mapped paired reads (singletons) = 221,501 number of mapped bases = 1,879,058,792 bp number of sequenced bases = 1,877,813,449 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,102,187 duplication rate = 10.56% >>>>>>> Insert size mean insert size = 98,196.3601 std insert size = 3,034,004.8892 median insert size = 268 >>>>>>> Mapping quality mean mapping quality = 53.4615 >>>>>>> ACTG content number of A's = 536,296,893 bp (28.56%) number of C's = 373,343,974 bp (19.88%) number of T's = 546,962,055 bp (29.13%) number of G's = 421,062,040 bp (22.42%) number of N's = 148,487 bp (0.01%) GC percentage = 42.3% >>>>>>> Mismatches and indels general error rate = 0.0129 number of mismatches = 23,455,492 number of insertions = 309,223 mapped reads with insertion percentage = 2.12% number of deletions = 640,417 mapped reads with deletion percentage = 4.46% homopolymer indels = 47.64% >>>>>>> Coverage mean coverageData = 0.607X std coverageData = 8.0422X There is a 29.24% of reference with a coverageData >= 1X There is a 14% of reference with a coverageData >= 2X There is a 6.57% of reference with a coverageData >= 3X There is a 3.42% of reference with a coverageData >= 4X There is a 1.76% of reference with a coverageData >= 5X There is a 0.96% of reference with a coverageData >= 6X There is a 0.54% of reference with a coverageData >= 7X There is a 0.31% of reference with a coverageData >= 8X There is a 0.19% of reference with a coverageData >= 9X There is a 0.12% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 161180342 0.6466597409199635 12.596005942639048 chr2 243199373 151362771 0.6223814195442026 8.211423975637958 chr3 198022430 135129068 0.6823927370247905 1.3726964873379777 chr4 191154276 93237974 0.48776295226584415 6.128727349204459 chr5 180915260 126625112 0.6999139376081377 1.3345811975293402 chr6 171115067 118950711 0.6951504217919046 6.809891717888597 chr7 159138663 93167463 0.5854483206258934 7.966090725534292 chr8 146364022 114278892 0.7807854036697625 3.0423771647067825 chr9 141213431 81061180 0.5740330748000876 13.450121082412235 chr10 135534747 103202530 0.7614470258316858 20.61591260983831 chr11 135006516 87221137 0.6460513135528955 6.995959729391116 chr12 133851895 78790943 0.5886427158913216 1.3267377155421198 chr13 115169878 59385676 0.51563548586897 1.1125165210143169 chr14 107349540 59195603 0.5514285669039662 1.2390657764566768 chr15 102531392 52621546 0.5132237549257109 1.132605098253516 chr16 90354753 60345424 0.6678721594203241 9.219554333043419 chr17 81195210 46223986 0.5692944940963882 9.350414487878899 chr18 78077248 68972723 0.8833908054751111 8.96822525297192 chr19 59128983 24236149 0.40988611287293747 5.4413885122413665 chr20 63025520 48617776 0.7713982526443257 2.332214797002174 chr21 48129895 20278037 0.4213189536357808 2.8729049937995685 chr22 51304566 13240995 0.2580860931559191 0.7982840214205387 chrMT 16571 943578 56.94152434976767 28.836348509489344 chrX 155270560 76517911 0.49280372918085696 2.2067024304859806 chrY 59373566 4271265 0.07193883217322672 5.971230629146429