BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779418.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 = 15,622,170 number of mapped reads = 15,221,618 (97.44%) number of supplementary alignments = 54,822 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,658,711 number of mapped paired reads (second in pair) = 7,562,907 number of mapped paired reads (both in pair) = 15,095,886 number of mapped paired reads (singletons) = 125,732 number of mapped bases = 1,210,340,028 bp number of sequenced bases = 1,210,083,956 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 481,702 duplication rate = 2.78% >>>>>>> Insert size mean insert size = 75,885.5627 std insert size = 2,621,896.5951 median insert size = 191 >>>>>>> Mapping quality mean mapping quality = 53.4563 >>>>>>> ACTG content number of A's = 367,140,304 bp (30.34%) number of C's = 237,538,648 bp (19.63%) number of T's = 362,373,563 bp (29.95%) number of G's = 242,763,839 bp (20.06%) number of N's = 267,602 bp (0.02%) GC percentage = 39.69% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 4,127,895 number of insertions = 106,973 mapped reads with insertion percentage = 0.7% number of deletions = 123,658 mapped reads with deletion percentage = 0.8% homopolymer indels = 46.81% >>>>>>> Coverage mean coverageData = 0.391X std coverageData = 1.5331X There is a 23.09% of reference with a coverageData >= 1X There is a 8.67% of reference with a coverageData >= 2X There is a 3.42% of reference with a coverageData >= 3X There is a 1.49% of reference with a coverageData >= 4X There is a 0.73% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.25% of reference with a coverageData >= 7X There is a 0.18% of reference with a coverageData >= 8X There is a 0.13% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% 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 0.01% 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 88915488 0.3567312596585266 3.4956494965414713 chr2 243199373 98513819 0.4050743132466875 0.9629639224156162 chr3 198022430 78659445 0.3972249254794015 0.8477118064895399 chr4 191154276 81064696 0.42407995100250856 0.8987793695963687 chr5 180915260 107257210 0.592858833467116 1.0550937932940028 chr6 171115067 59671230 0.34871990553584625 1.2449383974497719 chr7 159138663 124049269 0.7795042804902791 2.219300265607836 chr8 146364022 63723671 0.43537797150723284 0.9412558006532917 chr9 141213431 79256648 0.5612543186490526 2.0369822647150864 chr10 135534747 29895590 0.22057509724794042 2.0182503336848625 chr11 135006516 39265767 0.29084349528729414 0.8218235791612971 chr12 133851895 49628246 0.3707698422947243 0.8450867037202581 chr13 115169878 44305743 0.38469905299370033 0.8420516563827762 chr14 107349540 38765056 0.36111059255586936 0.8500224765132287 chr15 102531392 28875116 0.28162219820442896 0.7448356291775718 chr16 90354753 30363073 0.3360428974887464 0.8230275207615744 chr17 81195210 29206958 0.35971282049766234 1.0896626524772066 chr18 78077248 36809478 0.471449480391522 1.361490872443425 chr19 59128983 17673513 0.298897631978551 2.060913356731319 chr20 63025520 22173546 0.3518185331909995 0.836977520967136 chr21 48129895 17007067 0.35335765847816625 0.8744492026119289 chr22 51304566 10732655 0.20919492818631386 0.6457222259688484 chrMT 16571 13898 0.8386941041578662 0.9790055759417714 chrX 155270560 29270784 0.18851470620058303 0.630427130443463 chrY 59373566 5242062 0.08828949233064425 0.4371522874745758