BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714253.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 260,022 number of mapped reads = 93,903 (36.11%) number of supplementary alignments = 2,700 (1.04%) number of secondary alignments = 0 number of mapped bases = 12,121,942 bp number of sequenced bases = 11,814,410 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 67,518 duplication rate = 39.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.3833 >>>>>>> ACTG content number of A's = 3,264,820 bp (27.63%) number of C's = 2,385,006 bp (20.19%) number of T's = 3,098,005 bp (26.22%) number of G's = 3,066,476 bp (25.96%) number of N's = 103 bp (0%) GC percentage = 46.14% >>>>>>> Mismatches and indels general error rate = 0.049 number of mismatches = 541,502 number of insertions = 13,424 mapped reads with insertion percentage = 13.57% number of deletions = 47,558 mapped reads with deletion percentage = 46.79% homopolymer indels = 30.76% >>>>>>> Coverage mean coverageData = 0.0039X std coverageData = 0.9972X There is a 0.03% of reference with a coverageData >= 1X There is a 0.02% 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 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 0.01% 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 0.01% 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% 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 679505 0.0027261918035502105 0.4063357368586309 chr2 243199373 1591139 0.0065425292029844175 2.711422329098859 chr3 198022430 626990 0.003166257479013867 0.6402593371518316 chr4 191154276 485696 0.0025408586727089484 0.4184170113601202 chr5 180915260 768941 0.004250282701415016 0.7388536652701819 chr6 171115067 588862 0.0034413217393650087 0.669976500864853 chr7 159138663 561618 0.0035291109615518137 0.5630111248366532 chr8 146364022 744079 0.005083756170625046 1.2054183433363328 chr9 141213431 351247 0.002487348388270518 0.45689433892487796 chr10 135534747 621027 0.004582050092291093 0.6188700067971383 chr11 135006516 653255 0.004838692378373796 0.9751930891076966 chr12 133851895 485276 0.003625469777622498 0.6223593667280222 chr13 115169878 359026 0.00311736025282583 0.48684952836045287 chr14 107349540 511776 0.0047673795341833785 0.7601660692548942 chr15 102531392 283867 0.002768586229669056 0.2949445387413818 chr16 90354753 254741 0.002819342553014339 0.4537318424391413 chr17 81195210 373626 0.004601576866418598 1.258986119249194 chr18 78077248 233797 0.0029944318734184895 0.38171643533869326 chr19 59128983 181781 0.00307431298116526 0.4466087918825783 chr20 63025520 213970 0.003394973972447986 0.5135234844728039 chr21 48129895 107187 0.002227035816305022 0.35227362496762127 chr22 51304566 93899 0.0018302269626450012 0.22872405825230385 chrMT 16571 32318 1.9502745760666225 13.799185829442996 chrX 155270560 1281814 0.00825535761576438 0.9367835746301564 chrY 59373566 36505 6.148359018894031E-4 0.09975980205130143