BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094159.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 = 37,244 number of mapped reads = 949 (2.55%) number of supplementary alignments = 30 (0.08%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 320 number of mapped paired reads (second in pair) = 629 number of mapped paired reads (both in pair) = 540 number of mapped paired reads (singletons) = 409 number of mapped bases = 68,134 bp number of sequenced bases = 67,952 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 703 duplication rate = 26.45% >>>>>>> Insert size mean insert size = 79.832 std insert size = 69.7399 median insert size = 34 >>>>>>> Mapping quality mean mapping quality = 3.7181 >>>>>>> ACTG content number of A's = 10,495 bp (15.44%) number of C's = 6,803 bp (10.01%) number of T's = 7,733 bp (11.38%) number of G's = 42,921 bp (63.16%) number of N's = 0 bp (0%) GC percentage = 73.18% >>>>>>> Mismatches and indels general error rate = 0.0266 number of mismatches = 1,342 number of insertions = 83 mapped reads with insertion percentage = 5.27% number of deletions = 36 mapped reads with deletion percentage = 3.58% homopolymer indels = 61.34% >>>>>>> Coverage mean coverageData = 0X std coverageData = 0.0466X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 538 2.1584700485059175E-6 0.0017346512402657336 chr2 243199373 37559 1.5443707578966496E-4 0.1548777141622118 chr3 198022430 599 3.0249098549088604E-6 0.002953172041392093 chr4 191154276 208 1.0881263257746848E-6 0.001197245169180731 chr5 180915260 70 3.8692147914996225E-7 6.220300068660122E-4 chr6 171115067 785 4.5875562787232526E-6 0.0033800945986179613 chr7 159138663 488 3.0665081055758272E-6 0.0026014753549412723 chr8 146364022 6125 4.184771582732264E-5 0.03991795514211264 chr9 141213431 523 3.703613716460157E-6 0.0023994229054512253 chr10 135534747 134 9.88676357657568E-7 9.943215677921443E-4 chr11 135006516 628 4.651627333305898E-6 0.0031785522518129636 chr12 133851895 389 2.9061971815938803E-6 0.0032674103512761155 chr13 115169878 378 3.2821081915186193E-6 0.002212939908206565 chr14 107349540 125 1.1644204530359421E-6 0.0016855813684105278 chr15 102531392 115 1.1216077121044061E-6 0.0010590592306856808 chr16 90354753 302 3.3423808927904436E-6 0.002389730489171036 chr17 81195210 415 5.111138945265367E-6 0.0030934614756758273 chr18 78077248 30 3.8423485417928667E-7 6.198666844918054E-4 chr19 59128983 0 0.0 0.0 chr20 63025520 180 2.855985956165058E-6 0.0022462339665691895 chr21 48129895 0 0.0 0.0 chr22 51304566 82 1.5982982879145688E-6 0.0017879021285494684 chrMT 16571 6283 0.3791563574920041 1.5565216899401557 chrX 155270560 11988 7.720716663867253E-5 0.06253417370027256 chrY 59373566 190 3.200077286919233E-6 0.0022923467265811835