BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779088.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 = 31,033,794 number of mapped reads = 30,001,506 (96.67%) number of supplementary alignments = 220,564 (0.71%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,179,774 number of mapped paired reads (second in pair) = 14,821,732 number of mapped paired reads (both in pair) = 29,537,452 number of mapped paired reads (singletons) = 464,054 number of mapped bases = 2,994,730,503 bp number of sequenced bases = 2,993,969,511 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 796,734 duplication rate = 1.99% >>>>>>> Insert size mean insert size = 71,020.4372 std insert size = 2,584,636.2587 median insert size = 285 >>>>>>> Mapping quality mean mapping quality = 53.9505 >>>>>>> ACTG content number of A's = 896,414,092 bp (29.94%) number of C's = 595,633,593 bp (19.89%) number of T's = 893,664,600 bp (29.85%) number of G's = 607,265,612 bp (20.28%) number of N's = 991,614 bp (0.03%) GC percentage = 40.18% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 16,511,274 number of insertions = 295,748 mapped reads with insertion percentage = 0.97% number of deletions = 342,223 mapped reads with deletion percentage = 1.12% homopolymer indels = 47.19% >>>>>>> Coverage mean coverageData = 0.9674X std coverageData = 3.4109X There is a 46.78% of reference with a coverageData >= 1X There is a 23.87% of reference with a coverageData >= 2X There is a 11.9% of reference with a coverageData >= 3X There is a 5.91% of reference with a coverageData >= 4X There is a 2.95% of reference with a coverageData >= 5X There is a 1.5% of reference with a coverageData >= 6X There is a 0.79% of reference with a coverageData >= 7X There is a 0.43% of reference with a coverageData >= 8X There is a 0.25% of reference with a coverageData >= 9X There is a 0.15% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% 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 0.04% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% 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 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 262118052 1.0516244691723355 8.689142665200157 chr2 243199373 219340630 0.9018963630305084 2.1198069172008416 chr3 198022430 176850428 0.8930828088515024 1.323054842367185 chr4 191154276 217009378 1.1352577747201429 1.534826535045297 chr5 180915260 142512986 0.7877333620171123 1.2128467763564406 chr6 171115067 166608848 0.9736655627175134 1.9519153576820696 chr7 159138663 262249994 1.647933877639779 5.232780729796882 chr8 146364022 234821535 1.6043665088678691 1.9175674104552671 chr9 141213431 125196455 0.8865761147039901 2.516061650555009 chr10 135534747 77872749 0.5745592973291196 4.538607583698035 chr11 135006516 127968993 0.9478727160102406 1.56324880490403 chr12 133851895 117156797 0.8752718592441295 1.4323858770038007 chr13 115169878 88235378 0.7661324257024914 1.2688478851839868 chr14 107349540 74811062 0.6968922456491197 1.2360116667836822 chr15 102531392 89466552 0.8725771712920859 1.4654497314007708 chr16 90354753 72106670 0.7980395895720063 1.3660830925964726 chr17 81195210 75835376 0.9339882980781749 3.2434959987373135 chr18 78077248 86577238 1.1088664139391797 2.6005444063749654 chr19 59128983 39174630 0.6625283915334719 5.82962165448492 chr20 63025520 84295509 1.3374821659543625 1.7641245412170137 chr21 48129895 33481737 0.6956536472809675 1.2411487648235966 chr22 51304566 19247148 0.3751546792151014 0.8975367075363987 chrMT 16571 2250 0.13577937360448977 0.5051044716838434 chrX 155270560 199587189 1.2854155288678033 1.715205380198067 chrY 59373566 2202919 0.03710268977275173 0.4854954353998847