BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779099.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 = 17,691,036 number of mapped reads = 16,974,733 (95.95%) number of supplementary alignments = 96,248 (0.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,543,411 number of mapped paired reads (second in pair) = 8,431,322 number of mapped paired reads (both in pair) = 16,788,522 number of mapped paired reads (singletons) = 186,211 number of mapped bases = 1,691,799,763 bp number of sequenced bases = 1,691,409,232 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 533,467 duplication rate = 2.79% >>>>>>> Insert size mean insert size = 82,677.0993 std insert size = 2,741,618.4088 median insert size = 199 >>>>>>> Mapping quality mean mapping quality = 53.5219 >>>>>>> ACTG content number of A's = 517,698,001 bp (30.61%) number of C's = 327,023,431 bp (19.33%) number of T's = 513,102,372 bp (30.34%) number of G's = 332,902,428 bp (19.68%) number of N's = 683,000 bp (0.04%) GC percentage = 39.02% >>>>>>> Mismatches and indels general error rate = 0.0044 number of mismatches = 7,083,147 number of insertions = 141,744 mapped reads with insertion percentage = 0.82% number of deletions = 175,188 mapped reads with deletion percentage = 1.01% homopolymer indels = 46.51% >>>>>>> Coverage mean coverageData = 0.5465X std coverageData = 1.6571X There is a 26.33% of reference with a coverageData >= 1X There is a 12.82% of reference with a coverageData >= 2X There is a 6.32% of reference with a coverageData >= 3X There is a 3.39% of reference with a coverageData >= 4X There is a 1.91% of reference with a coverageData >= 5X There is a 1.13% of reference with a coverageData >= 6X There is a 0.69% of reference with a coverageData >= 7X There is a 0.44% of reference with a coverageData >= 8X There is a 0.29% of reference with a coverageData >= 9X There is a 0.2% of reference with a coverageData >= 10X There is a 0.14% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% 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 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% 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 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% 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 0.01% 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% 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 123914034 0.49714634010881764 2.1976615075283474 chr2 243199373 123762396 0.5088927429101554 1.4055900908871863 chr3 198022430 96900307 0.48934005607344583 1.136942450186015 chr4 191154276 148763682 0.7782388399200654 1.5353963358106582 chr5 180915260 100727460 0.5567659687745522 1.206169611772631 chr6 171115067 98982230 0.5784542047369797 1.261639604740172 chr7 159138663 166517829 1.046369410556126 3.368924333770704 chr8 146364022 139544033 0.953403924633883 1.6454989325309342 chr9 141213431 65760230 0.4656797128596075 1.2468550570979795 chr10 135534747 49041011 0.3618334935173487 2.945289704873815 chr11 135006516 62287959 0.46137002009591893 1.134914886816673 chr12 133851895 57444614 0.42916548921477726 1.0781699146588375 chr13 115169878 53634542 0.46569939059933707 1.1265076039122854 chr14 107349540 48891840 0.4554452678604864 1.1341484119044818 chr15 102531392 39762248 0.38780560006441733 1.0962997272202457 chr16 90354753 31945169 0.35355272345219074 1.015572468161839 chr17 81195210 29044863 0.35771645888963155 1.2960946289570379 chr18 78077248 48569695 0.6220723225285809 1.3526825117450545 chr19 59128983 16498622 0.27902766397994705 1.4556096432141445 chr20 63025520 37359996 0.5927756883243486 1.3495716297822355 chr21 48129895 16667992 0.34631266076936174 0.9824851157037949 chr22 51304566 8519542 0.16605816332214954 0.6639799545578041 chrMT 16571 811 0.04894092088588498 0.2601287047650802 chrX 155270560 126205118 0.8128077724457231 1.6385445440436324 chrY 59373566 1053540 0.017744260130846783 0.280466661226121