BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618603.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 48,398,738 number of mapped reads = 44,151,328 (91.22%) number of supplementary alignments = 95,576 (0.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 22,633,324 number of mapped paired reads (second in pair) = 21,518,004 number of mapped paired reads (both in pair) = 42,116,676 number of mapped paired reads (singletons) = 2,034,652 number of mapped bases = 4,155,611,723 bp number of sequenced bases = 4,152,836,856 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,784,134 duplication rate = 27.55% >>>>>>> Insert size mean insert size = 66,800.1585 std insert size = 2,636,089.645 median insert size = 222 >>>>>>> Mapping quality mean mapping quality = 52.3046 >>>>>>> ACTG content number of A's = 1,105,123,140 bp (26.61%) number of C's = 945,713,054 bp (22.77%) number of T's = 1,114,370,931 bp (26.83%) number of G's = 986,374,272 bp (23.75%) number of N's = 1,255,459 bp (0.03%) GC percentage = 46.52% >>>>>>> Mismatches and indels general error rate = 0.0146 number of mismatches = 59,492,008 number of insertions = 750,129 mapped reads with insertion percentage = 1.67% number of deletions = 2,025,642 mapped reads with deletion percentage = 4.47% homopolymer indels = 52.3% >>>>>>> Coverage mean coverageData = 1.3424X std coverageData = 6.2035X There is a 22.16% of reference with a coverageData >= 1X There is a 15.43% of reference with a coverageData >= 2X There is a 11.8% of reference with a coverageData >= 3X There is a 9.46% of reference with a coverageData >= 4X There is a 7.79% of reference with a coverageData >= 5X There is a 6.54% of reference with a coverageData >= 6X There is a 5.57% of reference with a coverageData >= 7X There is a 4.8% of reference with a coverageData >= 8X There is a 4.18% of reference with a coverageData >= 9X There is a 3.67% of reference with a coverageData >= 10X There is a 3.24% of reference with a coverageData >= 11X There is a 2.88% of reference with a coverageData >= 12X There is a 2.58% of reference with a coverageData >= 13X There is a 2.32% of reference with a coverageData >= 14X There is a 2.09% of reference with a coverageData >= 15X There is a 1.89% of reference with a coverageData >= 16X There is a 1.72% of reference with a coverageData >= 17X There is a 1.57% of reference with a coverageData >= 18X There is a 1.44% of reference with a coverageData >= 19X There is a 1.32% of reference with a coverageData >= 20X There is a 1.21% of reference with a coverageData >= 21X There is a 1.12% of reference with a coverageData >= 22X There is a 1.03% of reference with a coverageData >= 23X There is a 0.95% of reference with a coverageData >= 24X There is a 0.88% of reference with a coverageData >= 25X There is a 0.82% of reference with a coverageData >= 26X There is a 0.76% of reference with a coverageData >= 27X There is a 0.71% of reference with a coverageData >= 28X There is a 0.66% of reference with a coverageData >= 29X There is a 0.62% of reference with a coverageData >= 30X There is a 0.58% of reference with a coverageData >= 31X There is a 0.54% of reference with a coverageData >= 32X There is a 0.51% of reference with a coverageData >= 33X There is a 0.48% of reference with a coverageData >= 34X There is a 0.45% of reference with a coverageData >= 35X There is a 0.42% of reference with a coverageData >= 36X There is a 0.4% of reference with a coverageData >= 37X There is a 0.38% of reference with a coverageData >= 38X There is a 0.36% of reference with a coverageData >= 39X There is a 0.34% of reference with a coverageData >= 40X There is a 0.32% of reference with a coverageData >= 41X There is a 0.3% of reference with a coverageData >= 42X There is a 0.28% of reference with a coverageData >= 43X There is a 0.27% of reference with a coverageData >= 44X There is a 0.26% of reference with a coverageData >= 45X There is a 0.24% of reference with a coverageData >= 46X There is a 0.23% of reference with a coverageData >= 47X There is a 0.22% of reference with a coverageData >= 48X There is a 0.21% of reference with a coverageData >= 49X There is a 0.2% of reference with a coverageData >= 50X There is a 0.19% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 406663859 1.631546021303594 6.863010002773637 chr2 243199373 363890702 1.4962649677554885 6.413634200088567 chr3 198022430 269230214 1.3595945368411042 5.134951329117333 chr4 191154276 184032386 0.9627427115467718 5.426332240297461 chr5 180915260 234945551 1.2986497158946129 6.210803174701914 chr6 171115067 233946749 1.367189652562857 5.369916313019621 chr7 159138663 209044465 1.3135994802218491 5.422403992802476 chr8 146364022 209101738 1.4286416507466568 5.85705799431303 chr9 141213431 197590122 1.3992303749067607 6.784657488808591 chr10 135534747 226074493 1.6680187037203087 6.8153035118788585 chr11 135006516 226602430 1.6784555050661407 8.276788974253016 chr12 133851895 197797661 1.477735231167254 6.450581891289162 chr13 115169878 106667649 0.9261766258014096 4.169153264104274 chr14 107349540 140485242 1.3086711130760318 5.621158439594089 chr15 102531392 154092372 1.5028799374927047 6.296340391465114 chr16 90354753 170166635 1.8833169185908791 8.585478576451404 chr17 81195210 167687950 2.065244366016173 7.979082402589685 chr18 78077248 100346885 1.2852256908440216 5.59879011574292 chr19 59128983 3671023 0.06208500152962212 1.971327022783609 chr20 63025520 142104356 2.2547113613659993 7.544218488820064 chr21 48129895 62550157 1.2996113330394758 9.1722015058328 chr22 51304566 103452433 2.0164371529816663 8.058388267401304 chrMT 16571 11009 0.6643533884497013 3.238895360537572 chrX 155270560 8277398 0.053309513406791346 1.731968220151381 chrY 59373566 37178244 0.6261750220628487 4.62735555317088