BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779304.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 = 20,442,556 number of mapped reads = 19,558,529 (95.68%) number of supplementary alignments = 46,911 (0.23%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,869,208 number of mapped paired reads (second in pair) = 9,689,321 number of mapped paired reads (both in pair) = 19,347,308 number of mapped paired reads (singletons) = 211,221 number of mapped bases = 1,557,350,765 bp number of sequenced bases = 1,557,055,210 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 852,110 duplication rate = 3.98% >>>>>>> Insert size mean insert size = 34,743.0871 std insert size = 1,774,224.0029 median insert size = 218 >>>>>>> Mapping quality mean mapping quality = 53.0483 >>>>>>> ACTG content number of A's = 481,402,558 bp (30.92%) number of C's = 294,862,376 bp (18.94%) number of T's = 480,829,858 bp (30.88%) number of G's = 299,552,476 bp (19.24%) number of N's = 407,942 bp (0.03%) GC percentage = 38.18% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 5,580,365 number of insertions = 111,773 mapped reads with insertion percentage = 0.57% number of deletions = 142,914 mapped reads with deletion percentage = 0.72% homopolymer indels = 46.86% >>>>>>> Coverage mean coverageData = 0.5031X std coverageData = 1.9854X There is a 18.93% of reference with a coverageData >= 1X There is a 9.23% of reference with a coverageData >= 2X There is a 5.51% of reference with a coverageData >= 3X There is a 3.66% of reference with a coverageData >= 4X There is a 2.58% of reference with a coverageData >= 5X There is a 1.89% of reference with a coverageData >= 6X There is a 1.43% of reference with a coverageData >= 7X There is a 1.1% of reference with a coverageData >= 8X There is a 0.87% of reference with a coverageData >= 9X There is a 0.69% of reference with a coverageData >= 10X There is a 0.56% of reference with a coverageData >= 11X There is a 0.46% of reference with a coverageData >= 12X There is a 0.38% of reference with a coverageData >= 13X There is a 0.32% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.23% of reference with a coverageData >= 16X There is a 0.2% of reference with a coverageData >= 17X There is a 0.17% of reference with a coverageData >= 18X There is a 0.15% of reference with a coverageData >= 19X There is a 0.13% of reference with a coverageData >= 20X There is a 0.11% of reference with a coverageData >= 21X There is a 0.1% of reference with a coverageData >= 22X There is a 0.09% of reference with a coverageData >= 23X There is a 0.08% of reference with a coverageData >= 24X There is a 0.07% of reference with a coverageData >= 25X There is a 0.07% of reference with a coverageData >= 26X There is a 0.06% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.05% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% 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 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% 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 122035767 0.4896106838586372 1.8247099632156303 chr2 243199373 152198205 0.6258166010978984 1.8834818531704505 chr3 198022430 98257382 0.49619319387202754 1.8801767396538347 chr4 191154276 140393310 0.7344502719886842 2.0041060190390376 chr5 180915260 77938079 0.43079881155409444 1.4513458549515557 chr6 171115067 112969550 0.6601963928752107 2.0198591067165013 chr7 159138663 175159070 1.1006694834428765 4.603015309300663 chr8 146364022 118166076 0.8073437336943364 2.310564617772357 chr9 141213431 45165717 0.31984009368060745 1.373289652150138 chr10 135534747 33581379 0.24776951846894288 1.618528593608833 chr11 135006516 67478417 0.4998160014735881 1.6963763783919088 chr12 133851895 58355987 0.4359743057802805 1.5923845397632845 chr13 115169878 52278804 0.45392775357459353 1.541784913162141 chr14 107349540 31172877 0.2903866844701896 1.1975139594148814 chr15 102531392 25592131 0.24960288259814126 1.0890380559317483 chr16 90354753 21486065 0.2377967321763361 1.0745577762625842 chr17 81195210 12610133 0.15530636597897832 0.8353444104101492 chr18 78077248 41091310 0.5262904501961955 1.6995780972331658 chr19 59128983 9548825 0.16149144658889195 0.8663812780767227 chr20 63025520 20423269 0.3240476080165622 1.4885012615828828 chr21 48129895 16985979 0.35291951083624845 1.3344302604076053 chr22 51304566 3744178 0.07297943032984627 0.4513372127681535 chrMT 16571 1906 0.11502021604007 0.4307350145953953 chrX 155270560 119731422 0.7711147689555573 2.619427943754261 chrY 59373566 984927 0.0165886448524921 0.2108950706420691