BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618647.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 = 77,260,458 number of mapped reads = 73,152,467 (94.68%) number of supplementary alignments = 119,178 (0.15%) number of secondary alignments = 0 number of mapped bases = 7,118,516,911 bp number of sequenced bases = 7,113,655,696 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,618,464 duplication rate = 41.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.0176 >>>>>>> ACTG content number of A's = 1,878,773,031 bp (26.41%) number of C's = 1,657,835,309 bp (23.3%) number of T's = 2,123,671,348 bp (29.85%) number of G's = 1,453,031,116 bp (20.43%) number of N's = 344,892 bp (0%) GC percentage = 43.73% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 59,119,924 number of insertions = 1,208,093 mapped reads with insertion percentage = 1.62% number of deletions = 3,248,166 mapped reads with deletion percentage = 4.34% homopolymer indels = 52.48% >>>>>>> Coverage mean coverageData = 2.2995X std coverageData = 55.7753X There is a 19.63% of reference with a coverageData >= 1X There is a 13.46% of reference with a coverageData >= 2X There is a 10.43% of reference with a coverageData >= 3X There is a 8.5% of reference with a coverageData >= 4X There is a 7.13% of reference with a coverageData >= 5X There is a 6.08% of reference with a coverageData >= 6X There is a 5.27% of reference with a coverageData >= 7X There is a 4.63% of reference with a coverageData >= 8X There is a 4.11% of reference with a coverageData >= 9X There is a 3.69% of reference with a coverageData >= 10X There is a 3.34% of reference with a coverageData >= 11X There is a 3.04% of reference with a coverageData >= 12X There is a 2.78% of reference with a coverageData >= 13X There is a 2.56% of reference with a coverageData >= 14X There is a 2.37% of reference with a coverageData >= 15X There is a 2.2% of reference with a coverageData >= 16X There is a 2.06% of reference with a coverageData >= 17X There is a 1.92% of reference with a coverageData >= 18X There is a 1.8% of reference with a coverageData >= 19X There is a 1.7% of reference with a coverageData >= 20X There is a 1.6% of reference with a coverageData >= 21X There is a 1.51% of reference with a coverageData >= 22X There is a 1.44% of reference with a coverageData >= 23X There is a 1.36% of reference with a coverageData >= 24X There is a 1.3% of reference with a coverageData >= 25X There is a 1.24% of reference with a coverageData >= 26X There is a 1.18% of reference with a coverageData >= 27X There is a 1.13% of reference with a coverageData >= 28X There is a 1.08% of reference with a coverageData >= 29X There is a 1.04% of reference with a coverageData >= 30X There is a 0.99% of reference with a coverageData >= 31X There is a 0.96% of reference with a coverageData >= 32X There is a 0.92% of reference with a coverageData >= 33X There is a 0.89% of reference with a coverageData >= 34X There is a 0.85% of reference with a coverageData >= 35X There is a 0.82% of reference with a coverageData >= 36X There is a 0.8% of reference with a coverageData >= 37X There is a 0.77% of reference with a coverageData >= 38X There is a 0.74% of reference with a coverageData >= 39X There is a 0.72% of reference with a coverageData >= 40X There is a 0.7% of reference with a coverageData >= 41X There is a 0.68% of reference with a coverageData >= 42X There is a 0.66% of reference with a coverageData >= 43X There is a 0.64% of reference with a coverageData >= 44X There is a 0.62% of reference with a coverageData >= 45X There is a 0.6% of reference with a coverageData >= 46X There is a 0.59% of reference with a coverageData >= 47X There is a 0.57% of reference with a coverageData >= 48X There is a 0.56% of reference with a coverageData >= 49X There is a 0.54% of reference with a coverageData >= 50X There is a 0.53% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 683014190 2.74027076546381 63.670717128040486 chr2 243199373 595016380 2.446619712296709 55.878617856510466 chr3 198022430 449939891 2.2721662944950225 48.04909913359476 chr4 191154276 382399225 2.0004743446073894 46.67759200318751 chr5 180915260 423127582 2.338816427094099 51.1335484940714 chr6 171115067 415870088 2.4303534182644477 54.96615884867481 chr7 159138663 340439091 2.139260721324522 51.88996079868287 chr8 146364022 374971480 2.5619101940229547 58.923703333101635 chr9 141213431 316560083 2.2417137007314833 46.07431157762827 chr10 135534747 392246044 2.8940626125933595 62.65661053046381 chr11 135006516 392926342 2.910425019782008 63.435327707061006 chr12 133851895 351706675 2.6275808422435856 70.58902665597282 chr13 115169878 208396598 1.809471379313261 93.96997127586859 chr14 107349540 229143232 2.13455252812448 45.06003445923439 chr15 102531392 241427356 2.354667690457182 59.618399597588834 chr16 90354753 273048665 3.0219623864170155 55.73340257086962 chr17 81195210 231035371 2.84543104205285 64.93977739430959 chr18 78077248 201264398 2.5777598872337304 63.090539617198864 chr19 59128983 145989055 2.4689931670226763 37.90408504959066 chr20 63025520 176608153 2.802168915068055 36.04793583704808 chr21 48129895 88386275 1.8364111328312684 36.76619670106075 chr22 51304566 115590074 2.2530172850502233 52.66136314444725 chrMT 16571 13943 0.8414096916299559 3.133990429003147 chrX 155270560 14735948 0.09490497103894002 6.809990360130073 chrY 59373566 74660772 1.2574749510581864 41.50535516411913