BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779311.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 = 14,827,198 number of mapped reads = 13,637,220 (91.97%) number of supplementary alignments = 34,554 (0.23%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,903,976 number of mapped paired reads (second in pair) = 6,733,244 number of mapped paired reads (both in pair) = 13,435,632 number of mapped paired reads (singletons) = 201,588 number of mapped bases = 1,085,344,968 bp number of sequenced bases = 1,085,133,462 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 464,791 duplication rate = 3.14% >>>>>>> Insert size mean insert size = 35,562.2685 std insert size = 1,771,479.1031 median insert size = 223 >>>>>>> Mapping quality mean mapping quality = 53.3154 >>>>>>> ACTG content number of A's = 333,241,242 bp (30.71%) number of C's = 207,589,995 bp (19.13%) number of T's = 332,767,119 bp (30.67%) number of G's = 211,252,892 bp (19.47%) number of N's = 282,214 bp (0.03%) GC percentage = 38.6% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 3,891,364 number of insertions = 79,531 mapped reads with insertion percentage = 0.58% number of deletions = 101,530 mapped reads with deletion percentage = 0.74% homopolymer indels = 46.98% >>>>>>> Coverage mean coverageData = 0.3506X std coverageData = 1.486X There is a 15.63% of reference with a coverageData >= 1X There is a 6.53% of reference with a coverageData >= 2X There is a 3.54% of reference with a coverageData >= 3X There is a 2.22% of reference with a coverageData >= 4X There is a 1.5% of reference with a coverageData >= 5X There is a 1.07% of reference with a coverageData >= 6X There is a 0.8% of reference with a coverageData >= 7X There is a 0.61% of reference with a coverageData >= 8X There is a 0.48% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.25% of reference with a coverageData >= 12X There is a 0.21% of reference with a coverageData >= 13X There is a 0.18% of reference with a coverageData >= 14X There is a 0.15% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% 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 73807529 0.29611773364448307 1.753648928200352 chr2 243199373 86266226 0.35471401482601683 1.343894440871552 chr3 198022430 80287240 0.4054451811342786 1.4419489902928706 chr4 191154276 87359603 0.4570109799688708 1.776501992846241 chr5 180915260 68005337 0.37589607974473793 1.3928066259060226 chr6 171115067 54122538 0.31629323442336027 1.1798687519154067 chr7 159138663 96634298 0.6072333157656351 1.996785082832379 chr8 146364022 76706163 0.5240779937025781 1.5643005136461439 chr9 141213431 34573677 0.24483278081388732 1.1628705684476062 chr10 135534747 31559075 0.23284859195553742 1.3935435897817656 chr11 135006516 46101290 0.3414745551985061 1.3579553062816296 chr12 133851895 44597442 0.33318498778071093 1.7334760558147975 chr13 115169878 26508224 0.23016629400267316 0.9901107524884529 chr14 107349540 38371075 0.35744051627980894 1.4509731437624935 chr15 102531392 23706611 0.23121319761268821 0.8947946736779238 chr16 90354753 24560346 0.27182129533351723 1.18784467310624 chr17 81195210 20360808 0.2507636595804112 1.1039278701712247 chr18 78077248 30034629 0.3846783764714658 1.7659345960629418 chr19 59128983 16455368 0.27829614454894314 1.333693047795286 chr20 63025520 26716122 0.42389371797329084 1.478798978253118 chr21 48129895 11723135 0.24357283555262274 1.0038208446461374 chr22 51304566 5953721 0.11604661074415872 0.6738142513172954 chrMT 16571 2559 0.15442640757950638 0.8010670189969117 chrX 155270560 80059592 0.5156134685158603 2.0903319092714034 chrY 59373566 872360 0.014692733800088746 0.19405462746142277