BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080823.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 = 1,555,251 number of mapped reads = 1,291,730 (83.06%) number of supplementary alignments = 18,427 (1.18%) number of secondary alignments = 0 number of mapped bases = 89,722,002 bp number of sequenced bases = 89,691,247 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 53,431 duplication rate = 2.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5418 >>>>>>> ACTG content number of A's = 27,441,225 bp (30.6%) number of C's = 16,759,018 bp (18.69%) number of T's = 26,082,779 bp (29.08%) number of G's = 19,396,489 bp (21.63%) number of N's = 11,736 bp (0.01%) GC percentage = 40.31% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 876,635 number of insertions = 8,112 mapped reads with insertion percentage = 0.62% number of deletions = 17,437 mapped reads with deletion percentage = 1.33% homopolymer indels = 43.83% >>>>>>> Coverage mean coverageData = 0.029X std coverageData = 0.5404X There is a 2.62% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% 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 11052332 0.044342244587627325 1.1150882859112783 chr2 243199373 6724989 0.027652164218367456 0.31787471928324207 chr3 198022430 5313662 0.026833636977386853 0.1741472590945751 chr4 191154276 5279896 0.027621124206502187 0.18997578580963745 chr5 180915260 6756249 0.03734482652264933 0.20795271889718897 chr6 171115067 6116959 0.03574763524476778 0.3049867949376149 chr7 159138663 6191173 0.03890426677770945 0.661357793683957 chr8 146364022 4346921 0.02969938199703203 1.4776239046534132 chr9 141213431 3132439 0.02218230219192111 0.31535773508027704 chr10 135534747 3774052 0.027845641678882538 0.3487995564230101 chr11 135006516 3634420 0.02692033027502169 0.288439113663718 chr12 133851895 3444914 0.025736759274121595 0.17516388322848495 chr13 115169878 3541277 0.03074829166702773 0.18423440020504323 chr14 107349540 2359629 0.021980802153413977 0.19870599682135065 chr15 102531392 2117936 0.020656463924726587 0.15230129505464055 chr16 90354753 2029447 0.02246087707195658 0.21567655935375885 chr17 81195210 2130752 0.0262423362166315 0.20672904310887727 chr18 78077248 1396984 0.017892331451026554 0.6888997506331568 chr19 59128983 1490831 0.025213202127964893 0.6955989017840124 chr20 63025520 1513829 0.024019302022418854 0.1888509605070616 chr21 48129895 1406817 0.029229587972298715 0.20114581172200915 chr22 51304566 543073 0.010585276172105227 0.1066730371320949 chrMT 16571 35074 2.116589222135055 1.9905447490509924 chrX 155270560 5129280 0.03303446577380799 0.22046723839045138 chrY 59373566 259067 0.004363339065738447 0.14474954651109154