BamQC report ----------------------------------- >>>>>>> Input bam file = SRR536750.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP014781/SRP014781.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 = 25,228,568 number of mapped reads = 24,342,989 (96.49%) number of supplementary alignments = 530 (0%) number of secondary alignments = 0 number of mapped bases = 1,213,939,956 bp number of sequenced bases = 1,213,834,965 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 232,862 duplication rate = 0.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5609 >>>>>>> ACTG content number of A's = 378,515,050 bp (31.18%) number of C's = 226,852,409 bp (18.69%) number of T's = 376,970,123 bp (31.06%) number of G's = 231,011,261 bp (19.03%) number of N's = 486,122 bp (0.04%) GC percentage = 37.72% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 4,199,653 number of insertions = 66,050 mapped reads with insertion percentage = 0.27% number of deletions = 63,694 mapped reads with deletion percentage = 0.26% homopolymer indels = 48.33% >>>>>>> Coverage mean coverageData = 0.3921X std coverageData = 0.7034X There is a 29.4% of reference with a coverageData >= 1X There is a 7.61% of reference with a coverageData >= 2X There is a 1.73% of reference with a coverageData >= 3X There is a 0.37% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.02% 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 92735703 0.3720580619937553 0.7035575544746844 chr2 243199373 112452481 0.4623880383112665 0.7473527771974712 chr3 198022430 94198335 0.47569527856011057 0.7521216470194362 chr4 191154276 102412466 0.5357581747216578 0.7958166312047259 chr5 180915260 87595502 0.4841797314389068 0.7601520085761548 chr6 171115067 82910068 0.48452815671690674 0.7640853055353685 chr7 159138663 69833317 0.4388205586470209 0.740057300176322 chr8 146364022 67784661 0.4631237928129633 0.7459774390129665 chr9 141213431 50464635 0.3573642722412148 0.6790433223381214 chr10 135534747 51550925 0.3803520952453617 0.6761320895627521 chr11 135006516 53894402 0.3991985246104714 0.7170080796892471 chr12 133851895 56107472 0.4191757763309963 0.7238952076666076 chr13 115169878 51720400 0.449079228858782 0.7532531220759273 chr14 107349540 38735688 0.3608370189569513 0.6821341715582969 chr15 102531392 32228674 0.31432982008085875 0.6409817261577183 chr16 90354753 21389022 0.23672271009362397 0.5455375803737371 chr17 81195210 18873038 0.23244028804162217 0.5493837801012152 chr18 78077248 36820442 0.471589905422896 0.7535686093539997 chr19 59128983 8240440 0.13936380404175056 0.40983869897881703 chr20 63025520 18167845 0.2882617231876865 0.604193896992632 chr21 48129895 15712705 0.32646456012422215 0.6736322819825924 chr22 51304566 5921115 0.11541107276884478 0.37856897148912766 chrMT 16571 863 0.05207893307585541 0.22218622325773482 chrX 155270560 38687688 0.24916306091766527 0.5277977739038542 chrY 59373566 5502069 0.09266866335769693 0.34379720742113345