BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779096.sorted.bam outfile = /home/yangyx/scDNA/SRP052627/SRP052627.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 = 18,043,322 number of mapped reads = 17,519,765 (97.1%) number of supplementary alignments = 106,893 (0.59%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,835,376 number of mapped paired reads (second in pair) = 8,684,389 number of mapped paired reads (both in pair) = 17,306,998 number of mapped paired reads (singletons) = 212,767 number of mapped bases = 1,750,562,634 bp number of sequenced bases = 1,750,165,294 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 472,538 duplication rate = 2.42% >>>>>>> Insert size mean insert size = 62,541.0925 std insert size = 2,308,209.8002 median insert size = 219 >>>>>>> Mapping quality mean mapping quality = 53.4097 >>>>>>> ACTG content number of A's = 534,604,430 bp (30.55%) number of C's = 338,868,793 bp (19.36%) number of T's = 532,587,605 bp (30.43%) number of G's = 343,400,295 bp (19.62%) number of N's = 704,171 bp (0.04%) GC percentage = 38.98% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 7,321,141 number of insertions = 146,957 mapped reads with insertion percentage = 0.83% number of deletions = 178,121 mapped reads with deletion percentage = 1% homopolymer indels = 46.94% >>>>>>> Coverage mean coverageData = 0.5655X std coverageData = 1.6454X There is a 24.86% of reference with a coverageData >= 1X There is a 12.42% of reference with a coverageData >= 2X There is a 6.74% of reference with a coverageData >= 3X There is a 3.98% of reference with a coverageData >= 4X There is a 2.47% of reference with a coverageData >= 5X There is a 1.6% of reference with a coverageData >= 6X There is a 1.08% of reference with a coverageData >= 7X There is a 0.75% of reference with a coverageData >= 8X There is a 0.53% of reference with a coverageData >= 9X There is a 0.39% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.22% of reference with a coverageData >= 12X There is a 0.17% of reference with a coverageData >= 13X There is a 0.13% of reference with a coverageData >= 14X There is a 0.11% of reference with a coverageData >= 15X There is a 0.09% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 96688500 0.3879167867750267 1.25563394687298 chr2 243199373 105892112 0.43541276728538275 1.3920549155179414 chr3 198022430 127600206 0.6443724885105188 1.4591480745215701 chr4 191154276 85756169 0.44862281291578326 1.2556298586711603 chr5 180915260 112815079 0.6235796748157121 1.4924207543178252 chr6 171115067 95009606 0.5552381076997738 1.474073545701701 chr7 159138663 227666101 1.4306146395109527 3.3532132999322015 chr8 146364022 112037351 0.7654705676235106 1.5927028310829368 chr9 141213431 84044860 0.5951619432007144 1.5299260678527007 chr10 135534747 38954380 0.2874124965164837 2.4751724120850622 chr11 135006516 86247539 0.6388398245903923 1.5067279232004953 chr12 133851895 109838895 0.8206002238518925 1.7216372939168367 chr13 115169878 66898119 0.5808647205478502 1.4416300325030953 chr14 107349540 68327077 0.6364915676396936 1.6663303896195334 chr15 102531392 46287438 0.4514464994291699 1.2970790303764423 chr16 90354753 23187397 0.25662620094816707 0.8703272037510241 chr17 81195210 33652951 0.41446965898604116 1.1557124072226632 chr18 78077248 32391509 0.4148648912420684 1.2710949613186389 chr19 59128983 20732126 0.35062544539282875 1.0858603044838195 chr20 63025520 44443481 0.7051664309949367 1.5496677254055868 chr21 48129895 16815465 0.3493767231364207 1.131018690972362 chr22 51304566 8487262 0.1654289795571022 0.633387614644003 chrMT 16571 1035 0.062458511858065294 0.25176409040217423 chrX 155270560 105732970 0.6809595457116919 1.723132206267173 chrY 59373566 1055006 0.01776895125349217 0.33902070369314674