BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084885.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 = 1,591,654 number of mapped reads = 1,433,018 (90.03%) number of supplementary alignments = 14,497 (0.91%) number of secondary alignments = 0 number of mapped bases = 95,328,710 bp number of sequenced bases = 95,291,411 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,502 duplication rate = 3.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2274 >>>>>>> ACTG content number of A's = 25,712,770 bp (26.98%) number of C's = 17,823,091 bp (18.7%) number of T's = 30,022,842 bp (31.51%) number of G's = 21,719,239 bp (22.79%) number of N's = 13,469 bp (0.01%) GC percentage = 41.5% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 746,734 number of insertions = 7,825 mapped reads with insertion percentage = 0.54% number of deletions = 22,798 mapped reads with deletion percentage = 1.57% homopolymer indels = 47.95% >>>>>>> Coverage mean coverageData = 0.0308X std coverageData = 0.2691X There is a 2.69% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 7404781 0.029708174729081216 0.36183693746352996 chr2 243199373 8454255 0.034762651300091964 0.4583831547258577 chr3 198022430 7351125 0.03712268857623856 0.21596643473867863 chr4 191154276 5177882 0.027087450557475367 0.18845915174663808 chr5 180915260 5033161 0.027820544270284332 0.18842511215723032 chr6 171115067 5495127 0.03211363614169639 0.21806336044820898 chr7 159138663 5323197 0.033450054811633045 0.26265805320498276 chr8 146364022 5699002 0.038937178154341785 0.31403261450338066 chr9 141213431 6867490 0.04863198883681256 0.3245429697440378 chr10 135534747 2976848 0.02196372565627027 0.18997658563038514 chr11 135006516 4162587 0.03083248959627993 0.2590951704761301 chr12 133851895 3679403 0.027488613440997605 0.18878591485801346 chr13 115169878 2733651 0.023735815713896997 0.1710356093524012 chr14 107349540 2209763 0.020584745868496502 0.17371389837175386 chr15 102531392 2099591 0.020477543111869584 0.1648921329472481 chr16 90354753 1634539 0.018090238152717878 0.1603467236516054 chr17 81195210 2479287 0.030534892390819607 0.209221321683215 chr18 78077248 4109938 0.052639380937196965 0.44581960557502404 chr19 59128983 2181198 0.03688881305467405 0.3007859142448793 chr20 63025520 2069464 0.03283533400438426 0.20487345636491536 chr21 48129895 817541 0.016986137202252363 0.15182320852341358 chr22 51304566 897012 0.017484057851692967 0.14521808519321114 chrMT 16571 22905 1.3822340232937058 1.478441095685465 chrX 155270560 6222399 0.04007455759804048 0.24225014768643555 chrY 59373566 226564 0.0038159068970187843 0.0908382217525838