BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1163158.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 94,184,514 number of mapped reads = 90,926,518 (96.54%) number of supplementary alignments = 1,042,250 (1.11%) number of secondary alignments = 0 number of mapped bases = 9,042,861,243 bp number of sequenced bases = 9,041,301,326 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,481,183 duplication rate = 53.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.355 >>>>>>> ACTG content number of A's = 2,401,780,069 bp (26.56%) number of C's = 2,118,235,769 bp (23.43%) number of T's = 2,437,126,919 bp (26.96%) number of G's = 2,080,186,486 bp (23.01%) number of N's = 3,972,083 bp (0.04%) GC percentage = 46.44% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 74,351,441 number of insertions = 686,693 mapped reads with insertion percentage = 0.75% number of deletions = 768,543 mapped reads with deletion percentage = 0.83% homopolymer indels = 46.36% >>>>>>> Coverage mean coverageData = 2.9211X std coverageData = 28.5749X There is a 9.48% of reference with a coverageData >= 1X There is a 6.69% of reference with a coverageData >= 2X There is a 5.44% of reference with a coverageData >= 3X There is a 4.85% of reference with a coverageData >= 4X There is a 4.45% of reference with a coverageData >= 5X There is a 4.17% of reference with a coverageData >= 6X There is a 3.94% of reference with a coverageData >= 7X There is a 3.76% of reference with a coverageData >= 8X There is a 3.6% of reference with a coverageData >= 9X There is a 3.46% of reference with a coverageData >= 10X There is a 3.34% of reference with a coverageData >= 11X There is a 3.23% of reference with a coverageData >= 12X There is a 3.13% of reference with a coverageData >= 13X There is a 3.03% of reference with a coverageData >= 14X There is a 2.95% of reference with a coverageData >= 15X There is a 2.87% of reference with a coverageData >= 16X There is a 2.79% of reference with a coverageData >= 17X There is a 2.72% of reference with a coverageData >= 18X There is a 2.65% of reference with a coverageData >= 19X There is a 2.59% of reference with a coverageData >= 20X There is a 2.53% of reference with a coverageData >= 21X There is a 2.47% of reference with a coverageData >= 22X There is a 2.42% of reference with a coverageData >= 23X There is a 2.36% of reference with a coverageData >= 24X There is a 2.31% of reference with a coverageData >= 25X There is a 2.26% of reference with a coverageData >= 26X There is a 2.22% of reference with a coverageData >= 27X There is a 2.17% of reference with a coverageData >= 28X There is a 2.13% of reference with a coverageData >= 29X There is a 2.09% of reference with a coverageData >= 30X There is a 2.05% of reference with a coverageData >= 31X There is a 2.01% of reference with a coverageData >= 32X There is a 1.97% of reference with a coverageData >= 33X There is a 1.94% of reference with a coverageData >= 34X There is a 1.9% of reference with a coverageData >= 35X There is a 1.87% of reference with a coverageData >= 36X There is a 1.84% of reference with a coverageData >= 37X There is a 1.8% of reference with a coverageData >= 38X There is a 1.77% of reference with a coverageData >= 39X There is a 1.74% of reference with a coverageData >= 40X There is a 1.71% of reference with a coverageData >= 41X There is a 1.69% of reference with a coverageData >= 42X There is a 1.66% of reference with a coverageData >= 43X There is a 1.63% of reference with a coverageData >= 44X There is a 1.6% of reference with a coverageData >= 45X There is a 1.58% of reference with a coverageData >= 46X There is a 1.55% of reference with a coverageData >= 47X There is a 1.53% of reference with a coverageData >= 48X There is a 1.51% of reference with a coverageData >= 49X There is a 1.48% of reference with a coverageData >= 50X There is a 1.46% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 947983135 3.803333091795988 33.57127782093917 chr2 243199373 627216952 2.579023721413953 25.687596887022035 chr3 198022430 450159058 2.2732730731564095 20.671662099569886 chr4 191154276 336666192 1.7612276274688201 20.18650706568896 chr5 180915260 455033596 2.515175314674948 34.24441888721185 chr6 171115067 455116289 2.6597090307658298 24.592217885646132 chr7 159138663 492361064 3.093912282020366 28.414365056160303 chr8 146364022 374545107 2.558997094244923 41.24482941860841 chr9 141213431 408400837 2.8920821065525986 25.98249546609524 chr10 135534747 367751941 2.7133406682789616 24.825779959515206 chr11 135006516 442776665 3.279668849465014 26.0867167134747 chr12 133851895 451103322 3.370167616976958 25.862690164210747 chr13 115169878 165579916 1.4377015837422351 16.34668518910734 chr14 107349540 234534800 2.1847769445495526 20.04525000504576 chr15 102531392 376344859 3.670533011002133 28.77054071757057 chr16 90354753 326877074 3.61770757095645 27.70167392374454 chr17 81195210 491602950 6.05458068277673 41.73646739383124 chr18 78077248 155370271 1.9899557807160417 24.47403402817711 chr19 59128983 555388549 9.392831075751802 56.91714053925271 chr20 63025520 185779586 2.947688269767548 24.679225991050927 chr21 48129895 105301191 2.1878541600807564 30.75262865594251 chr22 51304566 167278738 3.260503909145241 26.75449860321052 chrMT 16571 8203 0.49502142296783536 0.8451507109572446 chrX 155270560 456001454 2.9368185057102907 27.672942238984394 chrY 59373566 13679494 0.23039704234709432 17.474634285923944