BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094034.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 400,716 number of mapped reads = 370,289 (92.41%) number of supplementary alignments = 19,810 (4.94%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 186,195 number of mapped paired reads (second in pair) = 184,094 number of mapped paired reads (both in pair) = 365,614 number of mapped paired reads (singletons) = 4,675 number of mapped bases = 47,824,727 bp number of sequenced bases = 47,004,219 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 342,395 duplication rate = 45.57% >>>>>>> Insert size mean insert size = 576,385.1468 std insert size = 6,902,296.8212 median insert size = 166 >>>>>>> Mapping quality mean mapping quality = 45.5722 >>>>>>> ACTG content number of A's = 13,214,656 bp (28.11%) number of C's = 10,285,930 bp (21.88%) number of T's = 12,618,214 bp (26.84%) number of G's = 10,884,863 bp (23.16%) number of N's = 556 bp (0%) GC percentage = 45.04% >>>>>>> Mismatches and indels general error rate = 0.0341 number of mismatches = 1,557,436 number of insertions = 25,882 mapped reads with insertion percentage = 6.85% number of deletions = 123,336 mapped reads with deletion percentage = 32.13% homopolymer indels = 29.56% >>>>>>> Coverage mean coverageData = 0.0154X std coverageData = 5.0637X 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 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% 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 763881 0.003064710518815518 0.8867098638845036 chr2 243199373 1957014 0.008046953311840981 2.3503224209520805 chr3 198022430 616567 0.003113622027565261 0.7849103188326907 chr4 191154276 1168371 0.006112188670056222 2.005749831320184 chr5 180915260 738700 0.0040831270949725305 1.9136984895175464 chr6 171115067 565460 0.0033045599660724207 0.8585156759822568 chr7 159138663 1274437 0.008008343013413403 2.4794046119910087 chr8 146364022 941518 0.006432714728213741 1.7918842845646328 chr9 141213431 831813 0.005890466608661325 2.017972281071242 chr10 135534747 1352471 0.009978776881473797 3.050121959029648 chr11 135006516 1008802 0.007472246746964421 2.1344795983278564 chr12 133851895 886871 0.006625763497782381 1.4141782623999657 chr13 115169878 1524733 0.013238991188303595 3.5533296861814407 chr14 107349540 331227 0.0030854999471818883 0.7934926843342359 chr15 102531392 425463 0.004149587669696321 0.9726335032915014 chr16 90354753 334405 0.003701022789581418 0.8936265505383195 chr17 81195210 1070151 0.013179976996179947 2.373840010570913 chr18 78077248 169242 0.002167622506367028 0.4652621788802296 chr19 59128983 207247 0.0035049985554461505 0.6304914575142035 chr20 63025520 375507 0.005958015102453736 1.9641369576617966 chr21 48129895 191654 0.003982015751332929 0.5146092303594592 chr22 51304566 183195 0.0035707348152988956 0.3620427237533027 chrMT 16571 6856278 413.7516142658862 1724.3383684112387 chrX 155270560 23209119 0.14947533518266437 10.466265745862094 chrY 59373566 840601 0.014157832460324178 2.672454045905744