BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779411.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 = 14,091,416 number of mapped reads = 13,609,390 (96.58%) number of supplementary alignments = 50,773 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,858,420 number of mapped paired reads (second in pair) = 6,750,970 number of mapped paired reads (both in pair) = 13,473,714 number of mapped paired reads (singletons) = 135,676 number of mapped bases = 1,082,150,032 bp number of sequenced bases = 1,081,919,260 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 421,883 duplication rate = 2.78% >>>>>>> Insert size mean insert size = 141,952.3545 std insert size = 3,662,762.4941 median insert size = 191 >>>>>>> Mapping quality mean mapping quality = 53.1424 >>>>>>> ACTG content number of A's = 329,255,513 bp (30.43%) number of C's = 211,795,066 bp (19.58%) number of T's = 323,182,446 bp (29.87%) number of G's = 217,450,477 bp (20.1%) number of N's = 235,758 bp (0.02%) GC percentage = 39.67% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 3,664,300 number of insertions = 96,626 mapped reads with insertion percentage = 0.7% number of deletions = 111,111 mapped reads with deletion percentage = 0.81% homopolymer indels = 47.09% >>>>>>> Coverage mean coverageData = 0.3496X std coverageData = 1.4196X There is a 18.15% of reference with a coverageData >= 1X There is a 8.19% of reference with a coverageData >= 2X There is a 3.97% of reference with a coverageData >= 3X There is a 2.03% of reference with a coverageData >= 4X There is a 1.07% of reference with a coverageData >= 5X There is a 0.58% of reference with a coverageData >= 6X There is a 0.33% of reference with a coverageData >= 7X There is a 0.19% of reference with a coverageData >= 8X There is a 0.11% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% 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 81660457 0.3276238858397869 3.332182017995384 chr2 243199373 88918918 0.3656214936047553 1.025001876937321 chr3 198022430 89706795 0.4530133025839548 1.0822228470935213 chr4 191154276 103880954 0.5434403884326396 1.1924302751599178 chr5 180915260 86116948 0.47600709857200546 1.1216915439094421 chr6 171115067 49596281 0.2898416946533411 0.898320632770614 chr7 159138663 100848315 0.6337134741417301 1.552389114823528 chr8 146364022 52571788 0.3591851828176736 0.9997122863960988 chr9 141213431 35092401 0.2485061141245127 1.0361341539862827 chr10 135534747 36200396 0.26709310196299696 1.7872469741474315 chr11 135006516 51590906 0.3821364148083045 1.044423623130901 chr12 133851895 38941332 0.29092850721314034 0.843063867315691 chr13 115169878 34285168 0.29769214481585193 0.884034353143597 chr14 107349540 28984592 0.27000201398161555 0.8959571514552453 chr15 102531392 28356846 0.2765674536048433 0.8791904112429084 chr16 90354753 6571557 0.07273061772411685 0.48332507584394946 chr17 81195210 15363262 0.18921389574582048 0.7238223154659367 chr18 78077248 40477108 0.5184238563326412 1.4400891220763163 chr19 59128983 16107237 0.27240849043522364 1.793049966903251 chr20 63025520 29759025 0.47217420816202704 1.17736080416587 chr21 48129895 17630089 0.36630225351623974 0.9646790121965155 chr22 51304566 12640452 0.2463806437812962 0.8294546282052837 chrMT 16571 1141 0.06885522901454348 0.31444189621398677 chrX 155270560 32335154 0.20825038564941095 0.7577131799469998 chrY 59373566 4512910 0.0760087409942667 0.4245436044915369