BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779422.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 = 13,913,238 number of mapped reads = 13,224,381 (95.05%) number of supplementary alignments = 59,109 (0.42%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,672,364 number of mapped paired reads (second in pair) = 6,552,017 number of mapped paired reads (both in pair) = 13,068,694 number of mapped paired reads (singletons) = 155,687 number of mapped bases = 1,051,116,704 bp number of sequenced bases = 1,050,894,031 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 692,335 duplication rate = 4.35% >>>>>>> Insert size mean insert size = 61,881.2723 std insert size = 2,309,479.1047 median insert size = 201 >>>>>>> Mapping quality mean mapping quality = 52.944 >>>>>>> ACTG content number of A's = 326,881,982 bp (31.11%) number of C's = 198,126,281 bp (18.85%) number of T's = 321,692,941 bp (30.61%) number of G's = 203,960,986 bp (19.41%) number of N's = 231,841 bp (0.02%) GC percentage = 38.26% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 3,989,787 number of insertions = 98,168 mapped reads with insertion percentage = 0.74% number of deletions = 110,356 mapped reads with deletion percentage = 0.82% homopolymer indels = 46.93% >>>>>>> Coverage mean coverageData = 0.3395X std coverageData = 2.375X There is a 13.95% of reference with a coverageData >= 1X There is a 6.69% of reference with a coverageData >= 2X There is a 3.83% of reference with a coverageData >= 3X There is a 2.44% of reference with a coverageData >= 4X There is a 1.64% of reference with a coverageData >= 5X There is a 1.15% of reference with a coverageData >= 6X There is a 0.83% of reference with a coverageData >= 7X There is a 0.62% of reference with a coverageData >= 8X There is a 0.47% of reference with a coverageData >= 9X There is a 0.36% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.22% of reference with a coverageData >= 12X There is a 0.18% of reference with a coverageData >= 13X There is a 0.15% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% 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 61823735 0.2480384391900873 5.41981519595359 chr2 243199373 77300009 0.3178462511907874 1.3250058213225435 chr3 198022430 68228734 0.34455053399758806 1.4168378204709315 chr4 191154276 89175161 0.46650884754469213 1.621263234648046 chr5 180915260 102259877 0.5652363266647601 1.642744911206574 chr6 171115067 55745326 0.3257768411474835 1.5190675177720818 chr7 159138663 125235600 0.7869589805464182 3.6738568818327093 chr8 146364022 49474889 0.3380263012996459 1.2997035156780998 chr9 141213431 57233312 0.40529651885591533 1.9691361592777932 chr10 135534747 24021129 0.1772322561682282 4.1479230329090395 chr11 135006516 51150133 0.37887158720546493 1.450960827105276 chr12 133851895 47268073 0.35313712219016397 1.3316307857601164 chr13 115169878 39647874 0.34425558738544465 1.2560928993649345 chr14 107349540 36594754 0.3408934402513509 1.377602278504634 chr15 102531392 20904365 0.20388258261430803 0.9164805152433179 chr16 90354753 22326928 0.24710297199307268 1.0949428819875118 chr17 81195210 16007329 0.19714622328090536 1.2434306875005678 chr18 78077248 30775610 0.3941687340209532 1.8892363535546177 chr19 59128983 9369661 0.15846139278262236 3.5658574691544116 chr20 63025520 18413048 0.29215225832329506 1.175652905035652 chr21 48129895 14940860 0.31042785362403136 1.4563189154580414 chr22 51304566 6527035 0.1272213276299813 0.7928947160097946 chrMT 16571 27199 1.641361414519341 1.542770378096062 chrX 155270560 19375873 0.12478780909916214 0.7140105710489685 chrY 59373566 7290190 0.12278511282276695 0.68029299204102