BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779421.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 = 15,284,056 number of mapped reads = 14,126,753 (92.43%) number of supplementary alignments = 70,467 (0.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,116,832 number of mapped paired reads (second in pair) = 7,009,921 number of mapped paired reads (both in pair) = 13,971,794 number of mapped paired reads (singletons) = 154,959 number of mapped bases = 1,122,215,588 bp number of sequenced bases = 1,121,972,455 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,053,375 duplication rate = 5.83% >>>>>>> Insert size mean insert size = 46,375.6319 std insert size = 2,035,031.113 median insert size = 199 >>>>>>> Mapping quality mean mapping quality = 52.9144 >>>>>>> ACTG content number of A's = 350,246,990 bp (31.22%) number of C's = 210,170,760 bp (18.73%) number of T's = 345,141,658 bp (30.76%) number of G's = 216,161,566 bp (19.27%) number of N's = 251,481 bp (0.02%) GC percentage = 38% >>>>>>> Mismatches and indels general error rate = 0.0041 number of mismatches = 4,369,274 number of insertions = 106,644 mapped reads with insertion percentage = 0.75% number of deletions = 121,002 mapped reads with deletion percentage = 0.85% homopolymer indels = 47.07% >>>>>>> Coverage mean coverageData = 0.3625X std coverageData = 3.4747X There is a 13.48% of reference with a coverageData >= 1X There is a 6.53% of reference with a coverageData >= 2X There is a 3.84% of reference with a coverageData >= 3X There is a 2.54% of reference with a coverageData >= 4X There is a 1.79% of reference with a coverageData >= 5X There is a 1.31% of reference with a coverageData >= 6X There is a 1% of reference with a coverageData >= 7X There is a 0.78% of reference with a coverageData >= 8X There is a 0.62% of reference with a coverageData >= 9X There is a 0.5% of reference with a coverageData >= 10X There is a 0.41% of reference with a coverageData >= 11X There is a 0.34% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.24% of reference with a coverageData >= 14X There is a 0.21% of reference with a coverageData >= 15X There is a 0.18% of reference with a coverageData >= 16X There is a 0.16% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.07% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 91427649 0.3668101151892416 8.057688195135185 chr2 243199373 102314619 0.4207026430121594 2.204199589520972 chr3 198022430 65536105 0.33095293800808323 2.529567821986765 chr4 191154276 90742337 0.4747073353462415 1.9495074003248698 chr5 180915260 125349119 0.692860950480352 2.2498758734397986 chr6 171115067 40395900 0.23607447729895112 4.213356419514961 chr7 159138663 138297962 0.8690406177410199 5.789922951903856 chr8 146364022 51415990 0.3512884471021164 1.8882876857181512 chr9 141213431 31250023 0.2212963935420562 1.8879055017360489 chr10 135534747 26666878 0.19675307321745322 4.813906039573982 chr11 135006516 49584428 0.3672743321514941 1.759743637514734 chr12 133851895 43906978 0.3280265699637648 1.6361721665087579 chr13 115169878 43117356 0.3743804955667314 1.5755440486507335 chr14 107349540 32507130 0.30281573633198616 1.5747924566735547 chr15 102531392 21851623 0.21312129459824364 1.0755224459782888 chr16 90354753 18898825 0.20916248866288195 1.253829137146064 chr17 81195210 19196791 0.23642762916679444 1.5595500250847494 chr18 78077248 35235268 0.45128726873160285 2.7707431204505273 chr19 59128983 11148062 0.1885380304951296 5.123184475502948 chr20 63025520 18488141 0.2933437280644412 1.344363755286769 chr21 48129895 14184648 0.29471595564461545 1.3542634772250202 chr22 51304566 4477388 0.08727075091133214 0.5547358637716222 chrMT 16571 46876 2.8287972964818056 1.9336750545688712 chrX 155270560 40708951 0.2621807443729191 1.368298162745817 chrY 59373566 5466541 0.0920702825900671 0.64617304156331