BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975270.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 2,232,870 number of mapped reads = 2,208,621 (98.91%) number of supplementary alignments = 22,487 (1.01%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,106,383 number of mapped paired reads (second in pair) = 1,102,238 number of mapped paired reads (both in pair) = 2,201,118 number of mapped paired reads (singletons) = 7,503 number of mapped bases = 298,504,612 bp number of sequenced bases = 298,314,003 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 320,780 duplication rate = 14.67% >>>>>>> Insert size mean insert size = 75,066.9863 std insert size = 2,611,427.3906 median insert size = 169 >>>>>>> Mapping quality mean mapping quality = 53.8044 >>>>>>> ACTG content number of A's = 85,611,772 bp (28.7%) number of C's = 61,957,260 bp (20.77%) number of T's = 85,893,264 bp (28.79%) number of G's = 64,833,401 bp (21.73%) number of N's = 18,306 bp (0.01%) GC percentage = 42.5% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 2,866,634 number of insertions = 47,166 mapped reads with insertion percentage = 2.05% number of deletions = 101,639 mapped reads with deletion percentage = 4.45% homopolymer indels = 47.91% >>>>>>> Coverage mean coverageData = 0.0964X std coverageData = 0.9837X There is a 5.56% of reference with a coverageData >= 1X There is a 3.06% of reference with a coverageData >= 2X There is a 0.4% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.04% 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 0.01% 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% 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 27681998 0.1110608988211909 1.1546900811123402 chr2 243199373 24858070 0.10221272239875388 1.162379348604397 chr3 198022430 20354245 0.10278757310472354 0.4488378949872654 chr4 191154276 18117478 0.09477934984828694 0.5947890149094831 chr5 180915260 17927318 0.09909234853931062 0.4319209572582504 chr6 171115067 24065539 0.14063950896854688 0.8957024524828753 chr7 159138663 16973125 0.10665619956854859 1.0430749320242316 chr8 146364022 15017172 0.10260152594057576 0.5414156595401638 chr9 141213431 12799442 0.09063898461613046 1.7609431539566898 chr10 135534747 15681033 0.11569751187125468 2.0753745301688276 chr11 135006516 10767917 0.0797584984712886 1.0885646005443856 chr12 133851895 12894913 0.09633717176734778 0.4250284776317507 chr13 115169878 9500350 0.08248988507220611 0.3961163981064504 chr14 107349540 8639837 0.08048322330957357 0.3984887086617965 chr15 102531392 8656732 0.08443006411148694 0.3974417802549722 chr16 90354753 9694123 0.10728957446212044 1.2431137655696007 chr17 81195210 6529452 0.08041671423720685 0.8169627170298555 chr18 78077248 8536240 0.10933069772131312 1.6018280596101457 chr19 59128983 4277089 0.07233489877544486 0.752766636099169 chr20 63025520 6690064 0.1061484934991413 0.4772187828875601 chr21 48129895 3622913 0.07527365268509312 0.5053802725889265 chr22 51304566 3226534 0.06288980204997738 0.34619866545857575 chrMT 16571 29432 1.7761148995232636 1.9127190780751044 chrX 155270560 8492014 0.054691720053048044 0.4591366446422421 chrY 59373566 3471582 0.058470161620408655 1.2228017045954351