BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779211.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 = 14,035,392 number of mapped reads = 13,556,144 (96.59%) number of supplementary alignments = 27,243 (0.19%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,867,581 number of mapped paired reads (second in pair) = 6,688,563 number of mapped paired reads (both in pair) = 13,360,430 number of mapped paired reads (singletons) = 195,714 number of mapped bases = 1,078,594,877 bp number of sequenced bases = 1,078,386,508 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 207,211 duplication rate = 1.42% >>>>>>> Insert size mean insert size = 41,467.0871 std insert size = 1,957,097.32 median insert size = 278 >>>>>>> Mapping quality mean mapping quality = 52.8158 >>>>>>> ACTG content number of A's = 331,578,496 bp (30.75%) number of C's = 205,882,575 bp (19.09%) number of T's = 330,491,206 bp (30.65%) number of G's = 210,236,102 bp (19.5%) number of N's = 198,129 bp (0.02%) GC percentage = 38.59% >>>>>>> Mismatches and indels general error rate = 0.0045 number of mismatches = 4,681,602 number of insertions = 79,653 mapped reads with insertion percentage = 0.58% number of deletions = 100,929 mapped reads with deletion percentage = 0.73% homopolymer indels = 47.23% >>>>>>> Coverage mean coverageData = 0.3484X std coverageData = 1.0037X There is a 20.28% of reference with a coverageData >= 1X There is a 7.51% of reference with a coverageData >= 2X There is a 3.23% of reference with a coverageData >= 3X There is a 1.55% of reference with a coverageData >= 4X There is a 0.81% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.27% of reference with a coverageData >= 7X There is a 0.17% of reference with a coverageData >= 8X There is a 0.11% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% 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 81423718 0.3266740827899482 1.019567807599431 chr2 243199373 122697364 0.5045134881988368 1.0871294468574415 chr3 198022430 44796395 0.2262187924872955 0.6850328064913282 chr4 191154276 41996535 0.21969968906162476 0.6554806170040756 chr5 180915260 60814563 0.3361494381402652 0.8483962013741225 chr6 171115067 63232868 0.3695341918663422 0.9180125876829129 chr7 159138663 90702570 0.5699593567654895 2.030321242469589 chr8 146364022 76903582 0.5254268156145641 1.1071129491939922 chr9 141213431 47539162 0.33664759551093976 0.9057658189746947 chr10 135534747 26985048 0.1991005893123481 0.8826148205634405 chr11 135006516 63620058 0.47123694385239895 1.0634639351843636 chr12 133851895 38368657 0.2866500844085921 0.7866937974281373 chr13 115169878 52336647 0.45442999427332903 1.0185540119380037 chr14 107349540 35281366 0.3286587534515751 0.9220090806178118 chr15 102531392 30444522 0.29692878840462833 0.8556934606766983 chr16 90354753 18328226 0.2028473919905464 0.6222418687190925 chr17 81195210 17820726 0.21948001612410387 0.6817473757197527 chr18 78077248 40891510 0.5237314460673614 1.0539633955805285 chr19 59128983 10151021 0.1716758936983577 0.6396714011933156 chr20 63025520 18919601 0.30018952640136887 0.8296521877117805 chr21 48129895 11328906 0.23538189725948913 0.6851950761949337 chr22 51304566 4704479 0.09169708208817126 0.41083113598965004 chrMT 16571 36 0.0021724699776718365 0.04655910600374486 chrX 155270560 78690658 0.5067970257851843 1.218503307867392 chrY 59373566 616659 0.01038608662986488 0.14146940275754594