BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1781846.sorted.bam outfile = /home/yangyx/scDNA/SRP052954/SRP052954.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 = 143,114,406 number of mapped reads = 135,531,326 (94.7%) number of supplementary alignments = 447,584 (0.31%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 68,719,912 number of mapped paired reads (second in pair) = 66,811,414 number of mapped paired reads (both in pair) = 132,759,126 number of mapped paired reads (singletons) = 2,772,200 number of mapped bases = 13,417,540,270 bp number of sequenced bases = 13,414,479,779 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,417,231 duplication rate = 5.91% >>>>>>> Insert size mean insert size = 48,070.0273 std insert size = 2,171,097.9356 median insert size = 221 >>>>>>> Mapping quality mean mapping quality = 54.0514 >>>>>>> ACTG content number of A's = 3,998,740,342 bp (29.81%) number of C's = 2,695,548,017 bp (20.09%) number of T's = 3,979,536,026 bp (29.67%) number of G's = 2,740,083,048 bp (20.43%) number of N's = 572,346 bp (0%) GC percentage = 40.52% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 46,969,030 number of insertions = 1,387,987 mapped reads with insertion percentage = 1.01% number of deletions = 1,373,167 mapped reads with deletion percentage = 1% homopolymer indels = 47.61% >>>>>>> Coverage mean coverageData = 4.3343X std coverageData = 6.8414X There is a 81.58% of reference with a coverageData >= 1X There is a 69.8% of reference with a coverageData >= 2X There is a 57.66% of reference with a coverageData >= 3X There is a 46.53% of reference with a coverageData >= 4X There is a 36.98% of reference with a coverageData >= 5X There is a 29.11% of reference with a coverageData >= 6X There is a 22.81% of reference with a coverageData >= 7X There is a 17.84% of reference with a coverageData >= 8X There is a 13.96% of reference with a coverageData >= 9X There is a 10.95% of reference with a coverageData >= 10X There is a 8.62% of reference with a coverageData >= 11X There is a 6.81% of reference with a coverageData >= 12X There is a 5.4% of reference with a coverageData >= 13X There is a 4.31% of reference with a coverageData >= 14X There is a 3.45% of reference with a coverageData >= 15X There is a 2.77% of reference with a coverageData >= 16X There is a 2.24% of reference with a coverageData >= 17X There is a 1.82% of reference with a coverageData >= 18X There is a 1.49% of reference with a coverageData >= 19X There is a 1.22% of reference with a coverageData >= 20X There is a 1.01% of reference with a coverageData >= 21X There is a 0.84% of reference with a coverageData >= 22X There is a 0.7% of reference with a coverageData >= 23X There is a 0.58% of reference with a coverageData >= 24X There is a 0.49% of reference with a coverageData >= 25X There is a 0.42% of reference with a coverageData >= 26X There is a 0.35% of reference with a coverageData >= 27X There is a 0.3% of reference with a coverageData >= 28X There is a 0.26% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.17% of reference with a coverageData >= 32X There is a 0.15% of reference with a coverageData >= 33X There is a 0.13% of reference with a coverageData >= 34X There is a 0.11% of reference with a coverageData >= 35X There is a 0.1% of reference with a coverageData >= 36X There is a 0.09% of reference with a coverageData >= 37X There is a 0.08% of reference with a coverageData >= 38X There is a 0.07% of reference with a coverageData >= 39X There is a 0.07% of reference with a coverageData >= 40X There is a 0.06% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1007217716 4.040983777528883 6.425798976724737 chr2 243199373 1136062257 4.6713206657814865 16.23053998236514 chr3 198022430 918415235 4.637935384390546 4.404693149448784 chr4 191154276 863087272 4.515134529347384 4.775398910408748 chr5 180915260 804129744 4.444786713956578 4.232793470349686 chr6 171115067 797768338 4.662174710775177 4.988815861247281 chr7 159138663 695588754 4.370960148131947 4.815640702237266 chr8 146364022 668735449 4.56898792382188 4.423407414846829 chr9 141213431 541281717 3.8330753184518263 5.244212936248854 chr10 135534747 749795477 5.532127322302081 8.613957991752741 chr11 135006516 606483429 4.492253018365425 4.600998621260317 chr12 133851895 888601944 6.638695283320419 6.746422687116015 chr13 115169878 413942601 3.5941915385201675 3.9862976209726084 chr14 107349540 401686173 3.741852764343471 4.339719069730462 chr15 102531392 381325556 3.71911029940957 4.447087355789553 chr16 90354753 320514505 3.5472899250800896 4.392415216564714 chr17 81195210 286195345 3.5247811416461636 5.2896097654296 chr18 78077248 340934094 4.3666253964279065 5.1077773340531145 chr19 59128983 180256014 3.04852214353154 5.124873856675736 chr20 63025520 259939626 4.124355118371098 5.0670422032872295 chr21 48129895 163831259 3.4039396720063486 5.966388249571855 chr22 51304566 129356041 2.5213358397769117 3.8437855775157783 chrMT 16571 2393917 144.46424476495082 38.3975135538185 chrX 155270560 849813369 5.473113312658884 5.330300556954574 chrY 59373566 10184438 0.1715315195991428 1.909636490855254