BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080976.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 = 6,244,403 number of mapped reads = 5,587,335 (89.48%) number of supplementary alignments = 51,371 (0.82%) number of secondary alignments = 0 number of mapped bases = 378,643,118 bp number of sequenced bases = 378,505,902 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 406,397 duplication rate = 5.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8696 >>>>>>> ACTG content number of A's = 106,080,281 bp (28.03%) number of C's = 68,436,395 bp (18.08%) number of T's = 121,121,174 bp (32%) number of G's = 82,109,596 bp (21.69%) number of N's = 758,456 bp (0.2%) GC percentage = 39.77% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 3,774,292 number of insertions = 29,422 mapped reads with insertion percentage = 0.52% number of deletions = 83,273 mapped reads with deletion percentage = 1.47% homopolymer indels = 49.09% >>>>>>> Coverage mean coverageData = 0.1223X std coverageData = 0.7896X There is a 7.84% of reference with a coverageData >= 1X There is a 2.59% of reference with a coverageData >= 2X There is a 0.94% of reference with a coverageData >= 3X There is a 0.38% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 31589630 0.1267384204430929 1.0220803147527036 chr2 243199373 25792611 0.10605541733859651 0.7750615834763462 chr3 198022430 33253223 0.16792654751282468 0.5955221703240953 chr4 191154276 23803669 0.1245259561967633 0.5338864442494059 chr5 180915260 22012889 0.12167513674634191 0.502436625091961 chr6 171115067 33034749 0.19305575820509133 0.9559512901010231 chr7 159138663 19443420 0.12217910866826875 0.8832537939379264 chr8 146364022 28118644 0.192114452826392 1.4080072857594454 chr9 141213431 19663234 0.13924478614219069 1.0055195638147691 chr10 135534747 16638409 0.12276120602490223 0.6430262062545984 chr11 135006516 17255610 0.12781316421794042 0.6766997956745786 chr12 133851895 15595207 0.11651091678604923 0.5365928349822312 chr13 115169878 10227210 0.0888010839084157 0.42647457991702536 chr14 107349540 10925504 0.10177504253860799 0.6581548433420995 chr15 102531392 9452198 0.09218833194032906 0.43767445005506556 chr16 90354753 8483992 0.09389646607744033 0.5815560295244253 chr17 81195210 8154805 0.10043455765432469 0.4806111174144865 chr18 78077248 9836033 0.12597822351525503 1.685652995031456 chr19 59128983 7124821 0.12049625477238464 0.8332908739677711 chr20 63025520 6019869 0.09551478512196329 0.5023905507109779 chr21 48129895 6860079 0.14253259850244843 0.6915725038584849 chr22 51304566 3369721 0.06568072323231425 0.36520148480038206 chrMT 16571 33788 2.0389837668215556 2.3318927130713463 chrX 155270560 11193567 0.07209072344428977 0.4465949150213801 chrY 59373566 760236 0.012804283980517524 0.2428894596972288