BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1781823.sorted.bam outfile = /home/yangyx/scDNA/SRP052954/SRP052954.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 = 168,130,146 number of mapped reads = 163,763,058 (97.4%) number of supplementary alignments = 507,857 (0.3%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 82,474,663 number of mapped paired reads (second in pair) = 81,288,395 number of mapped paired reads (both in pair) = 161,958,124 number of mapped paired reads (singletons) = 1,804,934 number of mapped bases = 16,263,947,945 bp number of sequenced bases = 16,260,602,473 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,870,778 duplication rate = 6.37% >>>>>>> Insert size mean insert size = 34,388.4597 std insert size = 1,799,926.2259 median insert size = 198 >>>>>>> Mapping quality mean mapping quality = 53.9069 >>>>>>> ACTG content number of A's = 4,838,466,152 bp (29.76%) number of C's = 3,285,387,289 bp (20.2%) number of T's = 4,820,709,988 bp (29.65%) number of G's = 3,314,624,521 bp (20.38%) number of N's = 1,414,523 bp (0.01%) GC percentage = 40.59% >>>>>>> Mismatches and indels general error rate = 0.0046 number of mismatches = 71,935,349 number of insertions = 1,782,419 mapped reads with insertion percentage = 1.07% number of deletions = 1,509,805 mapped reads with deletion percentage = 0.91% homopolymer indels = 46.91% >>>>>>> Coverage mean coverageData = 5.2537X std coverageData = 6.8146X There is a 83.2% of reference with a coverageData >= 1X There is a 72.86% of reference with a coverageData >= 2X There is a 61.99% of reference with a coverageData >= 3X There is a 51.82% of reference with a coverageData >= 4X There is a 42.83% of reference with a coverageData >= 5X There is a 35.2% of reference with a coverageData >= 6X There is a 28.86% of reference with a coverageData >= 7X There is a 23.66% of reference with a coverageData >= 8X There is a 19.44% of reference with a coverageData >= 9X There is a 16.01% of reference with a coverageData >= 10X There is a 13.23% of reference with a coverageData >= 11X There is a 10.97% of reference with a coverageData >= 12X There is a 9.14% of reference with a coverageData >= 13X There is a 7.64% of reference with a coverageData >= 14X There is a 6.42% of reference with a coverageData >= 15X There is a 5.41% of reference with a coverageData >= 16X There is a 4.58% of reference with a coverageData >= 17X There is a 3.89% of reference with a coverageData >= 18X There is a 3.32% of reference with a coverageData >= 19X There is a 2.84% of reference with a coverageData >= 20X There is a 2.44% of reference with a coverageData >= 21X There is a 2.1% of reference with a coverageData >= 22X There is a 1.82% of reference with a coverageData >= 23X There is a 1.58% of reference with a coverageData >= 24X There is a 1.37% of reference with a coverageData >= 25X There is a 1.2% of reference with a coverageData >= 26X There is a 1.05% of reference with a coverageData >= 27X There is a 0.92% of reference with a coverageData >= 28X There is a 0.81% of reference with a coverageData >= 29X There is a 0.72% of reference with a coverageData >= 30X There is a 0.64% of reference with a coverageData >= 31X There is a 0.56% of reference with a coverageData >= 32X There is a 0.5% of reference with a coverageData >= 33X There is a 0.45% of reference with a coverageData >= 34X There is a 0.4% of reference with a coverageData >= 35X There is a 0.36% of reference with a coverageData >= 36X There is a 0.32% of reference with a coverageData >= 37X There is a 0.29% of reference with a coverageData >= 38X There is a 0.26% of reference with a coverageData >= 39X There is a 0.24% of reference with a coverageData >= 40X There is a 0.22% of reference with a coverageData >= 41X There is a 0.2% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.13% of reference with a coverageData >= 47X There is a 0.12% of reference with a coverageData >= 48X There is a 0.11% of reference with a coverageData >= 49X There is a 0.1% of reference with a coverageData >= 50X There is a 0.09% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1283366842 5.148901281975141 8.912797716381165 chr2 243199373 1342314798 5.5194007346392295 8.276608808187671 chr3 198022430 1116721136 5.639366893942267 5.733156867480576 chr4 191154276 1061997520 5.555708939516477 5.970839921874037 chr5 180915260 991878837 5.482560382136919 5.380560355122123 chr6 171115067 957665855 5.5966191159542955 5.957123163163445 chr7 159138663 821356828 5.161265103754202 6.226531310862583 chr8 146364022 813919624 5.560926878601355 5.719997265730786 chr9 141213431 658285798 4.661637305590288 6.868164956928018 chr10 135534747 878587605 6.482379053690195 9.93089191348263 chr11 135006516 742365686 5.49873967564647 5.847282134773384 chr12 133851895 1075231400 8.032993481339954 7.804973498238771 chr13 115169878 504165464 4.377580950463454 4.966938727116058 chr14 107349540 487011997 4.536693841445431 5.474143419378477 chr15 102531392 443743430 4.327878724205753 5.433262693118796 chr16 90354753 368133725 4.074314994807191 5.193795690703846 chr17 81195210 334454744 4.119143777077491 5.264586120522364 chr18 78077248 403521455 5.168233580671286 6.26454543124693 chr19 59128983 215304413 3.6412669739305343 6.127595599107021 chr20 63025520 298329171 4.73346623716869 6.41800673504167 chr21 48129895 188242178 3.911127959036686 7.628702698169675 chr22 51304566 138199834 2.6937141228326538 4.524934595720353 chrMT 16571 1388092 83.76633878462374 24.25716440238384 chrX 155270560 1122710421 7.230671551645077 7.3228897594704865 chrY 59373566 15051092 0.2534981981712198 2.6389436520168834