BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708611.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 2,796,735 number of mapped reads = 1,543,916 (55.2%) number of supplementary alignments = 398 (0.01%) number of secondary alignments = 0 number of mapped bases = 74,317,360 bp number of sequenced bases = 74,296,983 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,760 duplication rate = 3.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.4108 >>>>>>> ACTG content number of A's = 21,517,407 bp (28.96%) number of C's = 14,224,130 bp (19.14%) number of T's = 23,189,172 bp (31.21%) number of G's = 15,360,095 bp (20.67%) number of N's = 6,179 bp (0.01%) GC percentage = 39.82% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 510,576 number of insertions = 3,752 mapped reads with insertion percentage = 0.24% number of deletions = 12,916 mapped reads with deletion percentage = 0.83% homopolymer indels = 49.76% >>>>>>> Coverage mean coverageData = 0.024X std coverageData = 0.2329X There is a 1.83% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 6019853 0.02415180742919794 0.2778961227583715 chr2 243199373 6508260 0.026761006493219865 0.2764809109520324 chr3 198022430 4919155 0.024841403067319193 0.20628461032483159 chr4 191154276 4956454 0.02592907730716942 0.21215808922086626 chr5 180915260 4782228 0.026433524734176653 0.21175639580951824 chr6 171115067 3972713 0.023216617155051578 0.22773012753948615 chr7 159138663 4337011 0.02725303152760558 0.292483543063336 chr8 146364022 4598742 0.03141989361292627 0.2675690724788689 chr9 141213431 2988984 0.021166428567265673 0.22574339245839586 chr10 135534747 3208414 0.02367226169684738 0.21520129589666387 chr11 135006516 3226607 0.023899639036681755 0.21961772040485056 chr12 133851895 3223601 0.024083342264224202 0.20222766574380466 chr13 115169878 2477309 0.02151004275614497 0.1957128403854767 chr14 107349540 2245076 0.020913699304160968 0.1947351192126225 chr15 102531392 2125244 0.020727739656553185 0.1878244788854099 chr16 90354753 2085893 0.023085592409289195 0.19782202497210444 chr17 81195210 1776796 0.02188301502022102 0.19720072490042684 chr18 78077248 2062792 0.02641988611073997 0.33763286984480956 chr19 59128983 1365990 0.02310186867242415 0.28927543658983274 chr20 63025520 1462595 0.02320639321976241 0.2257614306946115 chr21 48129895 893845 0.01857151360916121 0.1818232641246932 chr22 51304566 722053 0.014073854557116808 0.14814497744050523 chrMT 16571 1008 0.06082915937481142 0.24866843593331434 chrX 155270560 4141477 0.026672648053822953 0.21846593502059722 chrY 59373566 215260 0.0036255191409591265 0.08915495935143679