BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779379.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 = 15,437,378 number of mapped reads = 15,136,962 (98.05%) number of supplementary alignments = 63,329 (0.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,616,566 number of mapped paired reads (second in pair) = 7,520,396 number of mapped paired reads (both in pair) = 15,018,646 number of mapped paired reads (singletons) = 118,316 number of mapped bases = 1,203,039,488 bp number of sequenced bases = 1,202,786,762 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 638,972 duplication rate = 3.97% >>>>>>> Insert size mean insert size = 63,217.9654 std insert size = 2,376,535.1446 median insert size = 168 >>>>>>> Mapping quality mean mapping quality = 51.6856 >>>>>>> ACTG content number of A's = 360,718,186 bp (29.99%) number of C's = 239,646,227 bp (19.92%) number of T's = 358,826,217 bp (29.83%) number of G's = 243,331,177 bp (20.23%) number of N's = 264,955 bp (0.02%) GC percentage = 40.15% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 3,704,918 number of insertions = 105,154 mapped reads with insertion percentage = 0.69% number of deletions = 120,576 mapped reads with deletion percentage = 0.79% homopolymer indels = 47.37% >>>>>>> Coverage mean coverageData = 0.3886X std coverageData = 1.6347X There is a 15.43% of reference with a coverageData >= 1X There is a 8.61% of reference with a coverageData >= 2X There is a 5.11% of reference with a coverageData >= 3X There is a 3.2% of reference with a coverageData >= 4X There is a 2.05% of reference with a coverageData >= 5X There is a 1.33% of reference with a coverageData >= 6X There is a 0.88% of reference with a coverageData >= 7X There is a 0.6% of reference with a coverageData >= 8X There is a 0.41% of reference with a coverageData >= 9X There is a 0.28% of reference with a coverageData >= 10X There is a 0.2% of reference with a coverageData >= 11X There is a 0.15% of reference with a coverageData >= 12X There is a 0.11% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% 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 0.01% 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 82072606 0.32927743839001306 3.426662473599373 chr2 243199373 53648441 0.2205944873056889 0.9635147762085624 chr3 198022430 88024783 0.4445192547127111 1.437671497284031 chr4 191154276 96733314 0.5060483920328311 1.3560137142529456 chr5 180915260 94510232 0.5224005537178014 1.4073977047972677 chr6 171115067 60855375 0.35564007347173 1.163533788485207 chr7 159138663 111677775 0.7017639390372408 2.160966745782023 chr8 146364022 87752932 0.5995526140980193 1.5881406253900168 chr9 141213431 36944157 0.2616192860578538 1.0541709639186183 chr10 135534747 45145332 0.33309046572389295 1.5558573773862925 chr11 135006516 81125375 0.6008997002781703 1.641538873658231 chr12 133851895 68023522 0.5081999175282501 1.4364882404635313 chr13 115169878 42239386 0.3667572349082457 1.1902971661791493 chr14 107349540 30027896 0.27972077011228924 1.081854504989587 chr15 102531392 26405663 0.2575373501219997 1.025835090690078 chr16 90354753 22975222 0.2542779570212538 1.0449325812263517 chr17 81195210 21421318 0.263824898045094 1.3185313934123515 chr18 78077248 62262027 0.7974413621750602 1.863146239436296 chr19 59128983 18511285 0.313066182788904 2.050587256766516 chr20 63025520 28276099 0.4486452313285158 1.4058712313287802 chr21 48129895 14510530 0.3014868409748245 1.0837796939093363 chr22 51304566 6924027 0.13495927438505181 0.7115664188331484 chrMT 16571 704 0.04248385734113813 0.24628999414954647 chrX 155270560 15560105 0.10021284781867212 0.6119423612460898 chrY 59373566 7411382 0.1248262905414844 0.6258027457490593