BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779162.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 = 5,125,028 number of mapped reads = 4,997,137 (97.5%) number of supplementary alignments = 29,011 (0.57%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,513,510 number of mapped paired reads (second in pair) = 2,483,627 number of mapped paired reads (both in pair) = 4,950,602 number of mapped paired reads (singletons) = 46,535 number of mapped bases = 499,313,353 bp number of sequenced bases = 499,201,425 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 62,207 duplication rate = 1.13% >>>>>>> Insert size mean insert size = 63,617.8859 std insert size = 2,354,347.3237 median insert size = 209 >>>>>>> Mapping quality mean mapping quality = 53.4296 >>>>>>> ACTG content number of A's = 153,040,187 bp (30.66%) number of C's = 96,085,767 bp (19.25%) number of T's = 152,490,769 bp (30.55%) number of G's = 97,378,810 bp (19.51%) number of N's = 205,892 bp (0.04%) GC percentage = 38.75% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 2,036,391 number of insertions = 41,280 mapped reads with insertion percentage = 0.81% number of deletions = 49,958 mapped reads with deletion percentage = 0.98% homopolymer indels = 46.84% >>>>>>> Coverage mean coverageData = 0.1613X std coverageData = 0.5516X There is a 11.54% of reference with a coverageData >= 1X There is a 3.23% of reference with a coverageData >= 2X There is a 0.84% of reference with a coverageData >= 3X There is a 0.27% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% 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 33834205 0.13574371395447798 0.5416154109065998 chr2 243199373 32773419 0.1347594716043943 0.4960492289911157 chr3 198022430 34715288 0.1753098777749571 0.5260064335886576 chr4 191154276 42283332 0.22120003216668824 0.5965642670352962 chr5 180915260 35886969 0.1983634161098406 0.5619440061180104 chr6 171115067 29868729 0.17455347167061566 0.531716576960225 chr7 159138663 42147554 0.2648479835475305 0.8879348221648644 chr8 146364022 42281239 0.2888772693059774 0.6919204325424332 chr9 141213431 20293068 0.14370494262688085 0.49641074469816193 chr10 135534747 10805514 0.07972504644878999 0.6139628271315309 chr11 135006516 21640791 0.16029441867828068 0.5124308107704588 chr12 133851895 23595575 0.17628121738582783 0.5389837628733957 chr13 115169878 17078954 0.148293584195687 0.4871455993569572 chr14 107349540 15031597 0.14002479190874967 0.4816557465454908 chr15 102531392 11529878 0.11245217464715587 0.43886992911427497 chr16 90354753 9349780 0.10347856299269613 0.40300608153012596 chr17 81195210 8347389 0.10280642170886682 0.4255215780556339 chr18 78077248 12669620 0.1622703197735658 0.5078822097757059 chr19 59128983 5198090 0.0879110334097916 0.40446906814314976 chr20 63025520 10044751 0.15937593216208293 0.5201437949034495 chr21 48129895 5228444 0.10863194278732584 0.4148107921612762 chr22 51304566 2854411 0.055636587979323325 0.2930219659901004 chrMT 16571 239 0.014422786796210247 0.1189796804297124 chrX 155270560 31474398 0.20270679773422598 0.5851903576299079 chrY 59373566 380119 0.006402158832770799 0.11936357705099189