BamQC report ----------------------------------- >>>>>>> Input bam file = SRR26104291.sorted.bam outfile = /mainsd2/zhouyj/SRP461548/SRP461548.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 = 162,355,664 number of mapped reads = 158,723,288 (97.76%) number of supplementary alignments = 154,596 (0.1%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 80,012,295 number of mapped paired reads (second in pair) = 78,710,993 number of mapped paired reads (both in pair) = 157,124,850 number of mapped paired reads (singletons) = 1,598,438 number of mapped bases = 13,570,019,820 bp number of sequenced bases = 13,566,563,593 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,557,116 duplication rate = 36.87% >>>>>>> Insert size mean insert size = 10,594.9499 std insert size = 997,469.4898 median insert size = 164 >>>>>>> Mapping quality mean mapping quality = 53.1617 >>>>>>> ACTG content number of A's = 4,236,664,261 bp (31.23%) number of C's = 2,549,015,498 bp (18.79%) number of T's = 4,285,344,401 bp (31.59%) number of G's = 2,488,402,566 bp (18.34%) number of N's = 7,136,867 bp (0.05%) GC percentage = 37.13% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 84,623,068 number of insertions = 1,276,856 mapped reads with insertion percentage = 0.79% number of deletions = 1,537,644 mapped reads with deletion percentage = 0.95% homopolymer indels = 44.3% >>>>>>> Coverage mean coverageData = 4.3835X std coverageData = 91.528X There is a 62.05% of reference with a coverageData >= 1X There is a 50.34% of reference with a coverageData >= 2X There is a 41.21% of reference with a coverageData >= 3X There is a 34.83% of reference with a coverageData >= 4X There is a 29.33% of reference with a coverageData >= 5X There is a 25.06% of reference with a coverageData >= 6X There is a 21.34% of reference with a coverageData >= 7X There is a 18.33% of reference with a coverageData >= 8X There is a 15.71% of reference with a coverageData >= 9X There is a 13.55% of reference with a coverageData >= 10X There is a 11.68% of reference with a coverageData >= 11X There is a 10.11% of reference with a coverageData >= 12X There is a 8.76% of reference with a coverageData >= 13X There is a 7.62% of reference with a coverageData >= 14X There is a 6.63% of reference with a coverageData >= 15X There is a 5.79% of reference with a coverageData >= 16X There is a 5.06% of reference with a coverageData >= 17X There is a 4.45% of reference with a coverageData >= 18X There is a 3.91% of reference with a coverageData >= 19X There is a 3.45% of reference with a coverageData >= 20X There is a 3.05% of reference with a coverageData >= 21X There is a 2.71% of reference with a coverageData >= 22X There is a 2.4% of reference with a coverageData >= 23X There is a 2.14% of reference with a coverageData >= 24X There is a 1.91% of reference with a coverageData >= 25X There is a 1.72% of reference with a coverageData >= 26X There is a 1.54% of reference with a coverageData >= 27X There is a 1.39% of reference with a coverageData >= 28X There is a 1.25% of reference with a coverageData >= 29X There is a 1.13% of reference with a coverageData >= 30X There is a 1.03% of reference with a coverageData >= 31X There is a 0.94% of reference with a coverageData >= 32X There is a 0.85% of reference with a coverageData >= 33X There is a 0.78% of reference with a coverageData >= 34X There is a 0.71% of reference with a coverageData >= 35X There is a 0.65% of reference with a coverageData >= 36X There is a 0.6% of reference with a coverageData >= 37X There is a 0.55% of reference with a coverageData >= 38X There is a 0.51% of reference with a coverageData >= 39X There is a 0.47% of reference with a coverageData >= 40X There is a 0.44% of reference with a coverageData >= 41X There is a 0.4% of reference with a coverageData >= 42X There is a 0.38% of reference with a coverageData >= 43X There is a 0.35% of reference with a coverageData >= 44X There is a 0.33% of reference with a coverageData >= 45X There is a 0.3% of reference with a coverageData >= 46X There is a 0.28% of reference with a coverageData >= 47X There is a 0.27% of reference with a coverageData >= 48X There is a 0.25% of reference with a coverageData >= 49X There is a 0.23% of reference with a coverageData >= 50X There is a 0.22% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1158006925 4.645954021514755 62.17958894718185 chr2 243199373 1386463299 5.700932867947813 14.802510755858037 chr3 198022430 978412077 4.940915415491063 7.637665030662114 chr4 191154276 1283670295 6.715362700021421 13.102625746497178 chr5 180915260 949639692 5.2490856326879225 10.38068658414802 chr6 171115067 1054272713 6.161191597464646 11.226854012048676 chr7 159138663 1060847394 6.666182648524576 40.0064557521624 chr8 146364022 834872309 5.704081492103298 206.11553783171337 chr9 141213431 332424598 2.354057936599529 16.96655289800857 chr10 135534747 486940842 3.5927380452482787 32.45836623750051 chr11 135006516 622195071 4.608629934572936 12.52170062931675 chr12 133851895 464980777 3.47384530491705 6.13250534114295 chr13 115169878 499446604 4.336607910620518 13.936194392531293 chr14 107349540 243791895 2.271010150579127 5.213874211528297 chr15 102531392 208068413 2.029314231879345 4.324264939742267 chr16 90354753 169118664 1.8717185138008179 14.9689248699221 chr17 81195210 102609259 1.2637353730595684 7.577262552888498 chr18 78077248 276725884 3.5442576562124732 19.45255325432684 chr19 59128983 63143822 1.0678996795869125 33.25906955085562 chr20 63025520 119733162 1.8997568286624211 4.903305626745948 chr21 48129895 122087971 2.5366348918899573 6.634309757935973 chr22 51304566 35651252 0.6948943296781811 3.47943333710071 chrMT 16571 535219331 32298.55355741959 6508.111700774122 chrX 155270560 566219547 3.6466639071824045 6.450114397399132 chrY 59373566 15478024 0.26068880551995144 8.921159295962466