BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013294.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,482,577 number of mapped reads = 1,101,744 (74.31%) number of supplementary alignments = 7,705 (0.52%) number of secondary alignments = 0 number of mapped bases = 69,341,727 bp number of sequenced bases = 69,306,037 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 134,043 duplication rate = 9.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2565 >>>>>>> ACTG content number of A's = 18,598,157 bp (26.83%) number of C's = 12,185,491 bp (17.58%) number of T's = 22,807,082 bp (32.91%) number of G's = 15,702,179 bp (22.66%) number of N's = 13,128 bp (0.02%) GC percentage = 40.24% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 688,173 number of insertions = 6,096 mapped reads with insertion percentage = 0.55% number of deletions = 20,281 mapped reads with deletion percentage = 1.82% homopolymer indels = 48.39% >>>>>>> Coverage mean coverageData = 0.0224X std coverageData = 0.2925X There is a 1.5% of reference with a coverageData >= 1X There is a 0.42% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 4913830 0.019714414272211583 0.2713173250828422 chr2 243199373 12665898 0.05208030696690982 0.4935271689512778 chr3 198022430 3854950 0.019467239140535747 0.20893846839914004 chr4 191154276 4217952 0.022065695250259535 0.27727576900562073 chr5 180915260 2988504 0.016518805544651127 0.20420137157781748 chr6 171115067 3209241 0.018754870954759348 0.2184419411520825 chr7 159138663 2896078 0.018198456273319324 0.2842301936647145 chr8 146364022 3057628 0.020890571044843247 0.28751194936994134 chr9 141213431 7227967 0.051184699279773184 0.42529043493101815 chr10 135534747 2433616 0.017955661215053584 0.33998584353576017 chr11 135006516 2225456 0.016484063628454792 0.2173193826373632 chr12 133851895 2229646 0.016657560208617143 0.21042910851377847 chr13 115169878 1458565 0.012664465963921573 0.16852241980796803 chr14 107349540 1870090 0.01742056836014388 0.24700721036675177 chr15 102531392 2162637 0.02109243771897684 0.2040604346714331 chr16 90354753 1338941 0.014818711307860031 0.2264379870492889 chr17 81195210 1922119 0.023672812718878368 0.23286480179797617 chr18 78077248 1430349 0.018319664648016282 0.5499448216558057 chr19 59128983 921367 0.015582324492203764 0.22836208953403744 chr20 63025520 1816359 0.02881942108530005 0.24584181465268337 chr21 48129895 761773 0.015827439473948574 0.25889096399559636 chr22 51304566 529075 0.010312434959492689 0.14580613474960938 chrMT 16571 143277 8.646249471969103 6.375841137543998 chrX 155270560 2856549 0.01839723512300078 0.22020324289178422 chrY 59373566 209860 0.0035345695759624748 0.18230446358128471