BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779174.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 = 33,033,076 number of mapped reads = 32,255,950 (97.65%) number of supplementary alignments = 195,976 (0.59%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 16,220,126 number of mapped paired reads (second in pair) = 16,035,824 number of mapped paired reads (both in pair) = 31,968,656 number of mapped paired reads (singletons) = 287,294 number of mapped bases = 3,222,224,155 bp number of sequenced bases = 3,221,499,133 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,414,145 duplication rate = 3.74% >>>>>>> Insert size mean insert size = 79,462.5174 std insert size = 2,699,427.7552 median insert size = 201 >>>>>>> Mapping quality mean mapping quality = 53.4337 >>>>>>> ACTG content number of A's = 982,638,984 bp (30.5%) number of C's = 626,982,518 bp (19.46%) number of T's = 972,784,744 bp (30.2%) number of G's = 637,791,517 bp (19.8%) number of N's = 1,301,370 bp (0.04%) GC percentage = 39.26% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 12,983,827 number of insertions = 266,800 mapped reads with insertion percentage = 0.82% number of deletions = 322,970 mapped reads with deletion percentage = 0.98% homopolymer indels = 46.44% >>>>>>> Coverage mean coverageData = 1.0409X std coverageData = 3.0427X There is a 35.54% of reference with a coverageData >= 1X There is a 21.22% of reference with a coverageData >= 2X There is a 13.2% of reference with a coverageData >= 3X There is a 8.7% of reference with a coverageData >= 4X There is a 5.94% of reference with a coverageData >= 5X There is a 4.18% of reference with a coverageData >= 6X There is a 3.02% of reference with a coverageData >= 7X There is a 2.22% of reference with a coverageData >= 8X There is a 1.67% of reference with a coverageData >= 9X There is a 1.27% of reference with a coverageData >= 10X There is a 0.98% of reference with a coverageData >= 11X There is a 0.77% of reference with a coverageData >= 12X There is a 0.61% of reference with a coverageData >= 13X There is a 0.49% of reference with a coverageData >= 14X There is a 0.4% of reference with a coverageData >= 15X There is a 0.33% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.22% of reference with a coverageData >= 18X There is a 0.19% of reference with a coverageData >= 19X There is a 0.16% of reference with a coverageData >= 20X There is a 0.14% of reference with a coverageData >= 21X There is a 0.12% of reference with a coverageData >= 22X There is a 0.1% of reference with a coverageData >= 23X There is a 0.09% of reference with a coverageData >= 24X There is a 0.08% of reference with a coverageData >= 25X There is a 0.07% of reference with a coverageData >= 26X There is a 0.06% of reference with a coverageData >= 27X There is a 0.06% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.05% of reference with a coverageData >= 30X There is a 0.05% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.04% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.03% of reference with a coverageData >= 40X There is a 0.03% of reference with a coverageData >= 41X There is a 0.03% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 163020683 0.6540432370678025 2.347080737433519 chr2 243199373 306085755 1.2585795400056397 2.7193790040122185 chr3 198022430 288109636 1.454934352638739 2.6230891345075578 chr4 191154276 212146724 1.1098194005348851 2.3246743298470944 chr5 180915260 213539557 1.1803291607352526 2.292411354955517 chr6 171115067 158601270 0.92686911083055 2.131329497104737 chr7 159138663 350355775 2.2015754587557392 8.657090185635672 chr8 146364022 166350955 1.1365563252969366 2.246910827276033 chr9 141213431 106365726 0.7532266955541927 1.9018725832439174 chr10 135534747 64579726 0.4764809573149533 3.321394451476707 chr11 135006516 156062381 1.1559618426121003 2.3355351771779342 chr12 133851895 134885887 1.0077248962369938 2.1992389077607157 chr13 115169878 117130265 1.017021699024462 2.2350736621240763 chr14 107349540 96103593 0.8952399143955344 2.244111146424578 chr15 102531392 98292206 0.9586547503422171 2.2851327932834034 chr16 90354753 67920642 0.7517107816121195 1.7960629979966993 chr17 81195210 58513080 0.7206469445672965 1.9450279143595588 chr18 78077248 73420031 0.9403511635041235 1.9857008635694797 chr19 59128983 35662898 0.6031373480582272 1.8999809778225853 chr20 63025520 91283718 1.4483612035251752 2.757906404604815 chr21 48129895 36316715 0.75455628980699 1.7148103692649639 chr22 51304566 18368632 0.35803113508454587 1.1692526872881768 chrMT 16571 2322 0.14012431355983346 0.5051560441337635 chrX 155270560 206538063 1.3301817356748118 2.898913897879551 chrY 59373566 2567915 0.0432501392959958 0.8190129024132787