BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975204.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/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 = 44,307,292 number of mapped reads = 43,496,727 (98.17%) number of supplementary alignments = 92,567 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 21,745,086 number of mapped paired reads (second in pair) = 21,751,641 number of mapped paired reads (both in pair) = 43,152,578 number of mapped paired reads (singletons) = 344,149 number of mapped bases = 4,130,727,406 bp number of sequenced bases = 4,129,237,250 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,965,707 duplication rate = 47.67% >>>>>>> Insert size mean insert size = 129,470.5313 std insert size = 3,552,108.0813 median insert size = 236 >>>>>>> Mapping quality mean mapping quality = 55.7797 >>>>>>> ACTG content number of A's = 1,114,523,706 bp (26.99%) number of C's = 907,466,187 bp (21.98%) number of T's = 1,157,020,189 bp (28.02%) number of G's = 950,015,471 bp (23.01%) number of N's = 211,697 bp (0.01%) GC percentage = 44.98% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 23,932,352 number of insertions = 466,773 mapped reads with insertion percentage = 1.06% number of deletions = 957,312 mapped reads with deletion percentage = 2.17% homopolymer indels = 45.73% >>>>>>> Coverage mean coverageData = 1.3343X std coverageData = 26.1571X There is a 7.7% of reference with a coverageData >= 1X There is a 3.84% of reference with a coverageData >= 2X There is a 2.42% of reference with a coverageData >= 3X There is a 1.88% of reference with a coverageData >= 4X There is a 1.6% of reference with a coverageData >= 5X There is a 1.44% of reference with a coverageData >= 6X There is a 1.33% of reference with a coverageData >= 7X There is a 1.25% of reference with a coverageData >= 8X There is a 1.18% of reference with a coverageData >= 9X There is a 1.13% of reference with a coverageData >= 10X There is a 1.08% of reference with a coverageData >= 11X There is a 1.04% of reference with a coverageData >= 12X There is a 1.01% of reference with a coverageData >= 13X There is a 0.98% of reference with a coverageData >= 14X There is a 0.95% of reference with a coverageData >= 15X There is a 0.92% of reference with a coverageData >= 16X There is a 0.89% of reference with a coverageData >= 17X There is a 0.87% of reference with a coverageData >= 18X There is a 0.85% of reference with a coverageData >= 19X There is a 0.83% of reference with a coverageData >= 20X There is a 0.81% of reference with a coverageData >= 21X There is a 0.79% of reference with a coverageData >= 22X There is a 0.77% of reference with a coverageData >= 23X There is a 0.76% of reference with a coverageData >= 24X There is a 0.74% of reference with a coverageData >= 25X There is a 0.73% of reference with a coverageData >= 26X There is a 0.71% of reference with a coverageData >= 27X There is a 0.7% of reference with a coverageData >= 28X There is a 0.69% of reference with a coverageData >= 29X There is a 0.67% of reference with a coverageData >= 30X There is a 0.66% of reference with a coverageData >= 31X There is a 0.65% of reference with a coverageData >= 32X There is a 0.64% of reference with a coverageData >= 33X There is a 0.63% of reference with a coverageData >= 34X There is a 0.62% of reference with a coverageData >= 35X There is a 0.61% of reference with a coverageData >= 36X There is a 0.6% of reference with a coverageData >= 37X There is a 0.59% of reference with a coverageData >= 38X There is a 0.58% of reference with a coverageData >= 39X There is a 0.57% of reference with a coverageData >= 40X There is a 0.56% of reference with a coverageData >= 41X There is a 0.55% of reference with a coverageData >= 42X There is a 0.55% of reference with a coverageData >= 43X There is a 0.54% of reference with a coverageData >= 44X There is a 0.53% of reference with a coverageData >= 45X There is a 0.52% of reference with a coverageData >= 46X There is a 0.52% of reference with a coverageData >= 47X There is a 0.51% of reference with a coverageData >= 48X There is a 0.5% of reference with a coverageData >= 49X There is a 0.5% of reference with a coverageData >= 50X There is a 0.49% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 573764858 2.3019595927105034 36.63609188963839 chr2 243199373 263486980 1.0834196517439212 20.50728402153248 chr3 198022430 274975856 1.3886096438671114 25.73801518695503 chr4 191154276 155268854 0.8122698442801248 17.36569722842983 chr5 180915260 287691286 1.5901991131096405 29.698796215074317 chr6 171115067 237488188 1.3878858955184816 26.929187897953696 chr7 159138663 164362654 1.0328266613626131 21.227993324291965 chr8 146364022 174552582 1.1925921385243157 22.640550609518375 chr9 141213431 135159225 0.9571272650403913 19.597701420356834 chr10 135534747 142273952 1.0497230794993109 19.417292872222443 chr11 135006516 217643269 1.6120945525325607 30.13786638278006 chr12 133851895 194179191 1.450701844751619 25.827121077017434 chr13 115169878 61597658 0.5348417404766201 20.52088857859966 chr14 107349540 133335821 1.2420716567579144 26.173420976934814 chr15 102531392 116049027 1.1318389883948907 21.32102038096167 chr16 90354753 103405692 1.1444410898893167 19.401499133434875 chr17 81195210 128742521 1.585592561433119 26.750958204587466 chr18 78077248 60574367 0.7758261023749198 16.37925184424406 chr19 59128983 185150517 3.131298858970735 46.934870798721704 chr20 63025520 78592845 1.2470003420836513 24.796581809467135 chr21 48129895 37388777 0.7768306371746707 18.794799465195446 chr22 51304566 52330313 1.0199932887065062 20.238828239179874 chrMT 16571 422470 25.494538651861685 33.24996695706855 chrX 155270560 350532498 2.2575593080877665 40.5124987977553 chrY 59373566 1758005 0.029609220372581294 1.9919973934306379