BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779274.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 = 11,079,276 number of mapped reads = 10,740,991 (96.95%) number of supplementary alignments = 24,760 (0.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,414,032 number of mapped paired reads (second in pair) = 5,326,959 number of mapped paired reads (both in pair) = 10,638,924 number of mapped paired reads (singletons) = 102,067 number of mapped bases = 854,778,290 bp number of sequenced bases = 854,616,928 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 124,158 duplication rate = 1.06% >>>>>>> Insert size mean insert size = 45,735.1202 std insert size = 2,045,294.9797 median insert size = 200 >>>>>>> Mapping quality mean mapping quality = 53.1442 >>>>>>> ACTG content number of A's = 259,572,219 bp (30.37%) number of C's = 166,689,464 bp (19.5%) number of T's = 258,669,087 bp (30.27%) number of G's = 169,524,423 bp (19.84%) number of N's = 161,735 bp (0.02%) GC percentage = 39.34% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 3,286,193 number of insertions = 61,163 mapped reads with insertion percentage = 0.56% number of deletions = 77,301 mapped reads with deletion percentage = 0.71% homopolymer indels = 46.56% >>>>>>> Coverage mean coverageData = 0.2761X std coverageData = 0.8015X There is a 18.13% of reference with a coverageData >= 1X There is a 5.78% of reference with a coverageData >= 2X There is a 2.03% of reference with a coverageData >= 3X There is a 0.8% of reference with a coverageData >= 4X There is a 0.35% of reference with a coverageData >= 5X There is a 0.17% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 66194869 0.26557554293916885 1.0094884492284237 chr2 243199373 68870344 0.28318471034873927 0.733757449118204 chr3 198022430 58217925 0.29399661947386463 0.7398679159478299 chr4 191154276 60506060 0.3165299843985703 0.7599734454503787 chr5 180915260 55383525 0.3061296487648416 0.734854558701258 chr6 171115067 46064384 0.269201215343591 0.7029071696517009 chr7 159138663 73440745 0.4614890160287447 1.3879672946281176 chr8 146364022 60838330 0.4156645135100209 0.8838434580773297 chr9 141213431 37368939 0.2646273710324339 0.7242441109898189 chr10 135534747 18369778 0.13553556122401586 0.857126300361931 chr11 135006516 40347140 0.29885327905210146 0.7478602417284763 chr12 133851895 33452589 0.2499224161152145 0.6653010495348076 chr13 115169878 28669317 0.24893068828292064 0.6700301083526309 chr14 107349540 26511160 0.2469610955016668 0.6891934161807549 chr15 102531392 20385811 0.198825068131329 0.5829948854547484 chr16 90354753 20614911 0.22815524712905805 0.6360901111282751 chr17 81195210 15067448 0.1855706512736404 0.582731382340959 chr18 78077248 19805735 0.2536684566546198 0.6935203908944566 chr19 59128983 10885208 0.18409259634991523 0.7686567269871993 chr20 63025520 20314745 0.32232570235041297 0.7686142786208643 chr21 48129895 9876702 0.2052092987113311 0.6157426682053158 chr22 51304566 5521693 0.10762576180841292 0.4169827440278767 chrMT 16571 2907 0.1754269506970008 0.44519743353507246 chrX 155270560 57457345 0.3700466141166748 0.8491582047003983 chrY 59373566 610680 0.010285385250399142 0.14562642523462188