BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818928.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,444,156 number of mapped reads = 2,413,803 (98.76%) number of supplementary alignments = 31,936 (1.31%) number of secondary alignments = 0 number of mapped bases = 223,706,206 bp number of sequenced bases = 223,582,235 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,185,652 duplication rate = 41.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2453 >>>>>>> ACTG content number of A's = 64,253,224 bp (28.74%) number of C's = 48,059,101 bp (21.5%) number of T's = 62,687,841 bp (28.04%) number of G's = 48,572,811 bp (21.72%) number of N's = 9,258 bp (0%) GC percentage = 43.22% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,398,980 number of insertions = 26,165 mapped reads with insertion percentage = 1.05% number of deletions = 68,007 mapped reads with deletion percentage = 2.75% homopolymer indels = 43.54% >>>>>>> Coverage mean coverageData = 0.0723X std coverageData = 0.7899X There is a 3% of reference with a coverageData >= 1X There is a 1.59% of reference with a coverageData >= 2X There is a 0.94% of reference with a coverageData >= 3X There is a 0.57% of reference with a coverageData >= 4X There is a 0.35% of reference with a coverageData >= 5X There is a 0.22% of reference with a coverageData >= 6X There is a 0.14% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 27371094 0.10981354385472122 1.3825556166631747 chr2 243199373 20526444 0.08440171430869602 1.1557631592587634 chr3 198022430 15779775 0.07968680618655169 0.5639585035429452 chr4 191154276 13629710 0.07130214549843499 0.580959498027692 chr5 180915260 11793825 0.06518977448336863 0.5224364333822148 chr6 171115067 12435122 0.0726711108379486 0.588155243611607 chr7 159138663 11941914 0.07504093458419969 0.7163460509192057 chr8 146364022 11230508 0.07672997671517937 0.6466767939356003 chr9 141213431 6066009 0.04295631766074716 0.7272638055192754 chr10 135534747 11112104 0.08198712319874696 0.9128812565303195 chr11 135006516 8579094 0.06354577730159336 0.5706746865962078 chr12 133851895 10637398 0.07947140382285958 0.5772490557559676 chr13 115169878 3706073 0.032179186644619 0.34989631297515505 chr14 107349540 5831564 0.05432313915830473 0.5029397593106928 chr15 102531392 6365577 0.06208417613212547 0.5088203396123183 chr16 90354753 6997994 0.07745020342206016 0.8977984379324772 chr17 81195210 5168227 0.06365187059679998 0.5559132458451926 chr18 78077248 5835123 0.07473525450077338 1.0033868312876524 chr19 59128983 3658962 0.061881023727399474 1.1273325869518307 chr20 63025520 5012221 0.07952684880664214 0.6096378822888184 chr21 48129895 3081030 0.06401489136845198 0.540571816942436 chr22 51304566 2818503 0.054936689260757024 0.5049348868482288 chrMT 16571 16429 0.99143081286585 2.03417655960786 chrX 155270560 13455091 0.08665577685815005 0.6989846989235029 chrY 59373566 656415 0.011055677538384675 0.6879460464055219