BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695931.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 29,781,062 number of mapped reads = 25,536,691 (85.75%) number of supplementary alignments = 795,153 (2.67%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,111,458 number of mapped paired reads (second in pair) = 12,425,233 number of mapped paired reads (both in pair) = 23,854,620 number of mapped paired reads (singletons) = 1,682,071 number of mapped bases = 2,112,767,586 bp number of sequenced bases = 2,111,935,755 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,969,639 duplication rate = 21.84% >>>>>>> Insert size mean insert size = 140,548.6582 std insert size = 3,599,191.8203 median insert size = 317 >>>>>>> Mapping quality mean mapping quality = 51.7061 >>>>>>> ACTG content number of A's = 545,964,651 bp (25.85%) number of C's = 374,116,976 bp (17.71%) number of T's = 693,476,552 bp (32.84%) number of G's = 496,644,858 bp (23.52%) number of N's = 1,732,718 bp (0.08%) GC percentage = 41.23% >>>>>>> Mismatches and indels general error rate = 0.0127 number of mismatches = 26,565,824 number of insertions = 168,769 mapped reads with insertion percentage = 0.65% number of deletions = 472,932 mapped reads with deletion percentage = 1.83% homopolymer indels = 46.77% >>>>>>> Coverage mean coverageData = 0.6825X std coverageData = 6.9254X There is a 14.22% of reference with a coverageData >= 1X There is a 7.87% of reference with a coverageData >= 2X There is a 5.69% of reference with a coverageData >= 3X There is a 4.47% of reference with a coverageData >= 4X There is a 3.63% of reference with a coverageData >= 5X There is a 2.99% of reference with a coverageData >= 6X There is a 2.5% of reference with a coverageData >= 7X There is a 2.09% of reference with a coverageData >= 8X There is a 1.77% of reference with a coverageData >= 9X There is a 1.5% of reference with a coverageData >= 10X There is a 1.29% of reference with a coverageData >= 11X There is a 1.11% of reference with a coverageData >= 12X There is a 0.97% of reference with a coverageData >= 13X There is a 0.85% of reference with a coverageData >= 14X There is a 0.75% of reference with a coverageData >= 15X There is a 0.68% of reference with a coverageData >= 16X There is a 0.61% of reference with a coverageData >= 17X There is a 0.56% of reference with a coverageData >= 18X There is a 0.52% of reference with a coverageData >= 19X There is a 0.48% of reference with a coverageData >= 20X There is a 0.45% of reference with a coverageData >= 21X There is a 0.42% of reference with a coverageData >= 22X There is a 0.4% of reference with a coverageData >= 23X There is a 0.38% of reference with a coverageData >= 24X There is a 0.36% of reference with a coverageData >= 25X There is a 0.35% of reference with a coverageData >= 26X There is a 0.33% of reference with a coverageData >= 27X There is a 0.32% of reference with a coverageData >= 28X There is a 0.31% of reference with a coverageData >= 29X There is a 0.29% of reference with a coverageData >= 30X There is a 0.28% of reference with a coverageData >= 31X There is a 0.27% of reference with a coverageData >= 32X There is a 0.26% of reference with a coverageData >= 33X There is a 0.26% of reference with a coverageData >= 34X There is a 0.25% of reference with a coverageData >= 35X There is a 0.24% of reference with a coverageData >= 36X There is a 0.23% of reference with a coverageData >= 37X There is a 0.22% of reference with a coverageData >= 38X There is a 0.22% of reference with a coverageData >= 39X There is a 0.21% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.2% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 190825118 0.7655953563301252 10.094392065126648 chr2 243199373 183304347 0.7537204752579687 7.812672721281594 chr3 198022430 138298937 0.6984003630295821 4.284712508948093 chr4 191154276 144386211 0.7553386407113383 4.642856138348878 chr5 180915260 142339532 0.7867746037564769 4.674720858225443 chr6 171115067 119519019 0.6984716255290365 5.2271225992212 chr7 159138663 126375076 0.7941192518376254 9.884084480121308 chr8 146364022 106758223 0.7294020862586026 11.693705213480865 chr9 141213431 89665230 0.6349624774714241 5.728372124211747 chr10 135534747 100320968 0.7401863376038913 6.373214051167641 chr11 135006516 99569570 0.737516772894132 5.915097411445515 chr12 133851895 93663850 0.6997573698900564 4.3680577140517105 chr13 115169878 62284234 0.5408031603541336 3.7402201053678934 chr14 107349540 64133110 0.5974232400064313 4.15008035408458 chr15 102531392 60812138 0.5931075040900644 3.9513867106585505 chr16 90354753 59494809 0.6584579894762149 4.120498111180786 chr17 81195210 59043353 0.7271777854875922 4.63546725307489 chr18 78077248 55400153 0.7095556569821723 16.174183303368686 chr19 59128983 39689356 0.6712335302638301 7.436725234414295 chr20 63025520 43952995 0.6973840913966279 4.477613996051235 chr21 48129895 26525949 0.5511324926015317 4.169153916136482 chr22 51304566 22758904 0.4436038694879516 3.8611479514472893 chrMT 16571 3394462 204.84352181521936 164.5131152198868 chrX 155270560 64634010 0.4162669987150172 3.6812444911602333 chrY 59373566 15618032 0.2630468919451461 3.403590455709351