BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1779404.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 = 12,967,870
number of mapped reads = 12,379,865 (95.47%)
number of supplementary alignments = 44,801 (0.35%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 6,222,368
number of mapped paired reads (second in pair) = 6,157,497
number of mapped paired reads (both in pair) = 12,289,044
number of mapped paired reads (singletons) = 90,821
number of mapped bases = 982,891,143 bp
number of sequenced bases = 982,649,629 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 329,577
duplication rate = 2.51%
>>>>>>> Insert size
mean insert size = 102,711.2389
std insert size = 3,099,217.9754
median insert size = 189
>>>>>>> Mapping quality
mean mapping quality = 53.3098
>>>>>>> ACTG content
number of A's = 294,243,778 bp (29.94%)
number of C's = 196,740,130 bp (20.02%)
number of T's = 291,137,443 bp (29.63%)
number of G's = 200,313,763 bp (20.39%)
number of N's = 214,515 bp (0.02%)
GC percentage = 40.41%
>>>>>>> Mismatches and indels
general error rate = 0.0034
number of mismatches = 3,208,982
number of insertions = 93,579
mapped reads with insertion percentage = 0.75%
number of deletions = 113,314
mapped reads with deletion percentage = 0.9%
homopolymer indels = 47.07%
>>>>>>> Coverage
mean coverageData = 0.3175X
std coverageData = 0.9946X
There is a 17.12% of reference with a coverageData >= 1X
There is a 7.32% of reference with a coverageData >= 2X
There is a 3.39% of reference with a coverageData >= 3X
There is a 1.71% of reference with a coverageData >= 4X
There is a 0.9% of reference with a coverageData >= 5X
There is a 0.5% of reference with a coverageData >= 6X
There is a 0.28% of reference with a coverageData >= 7X
There is a 0.16% of reference with a coverageData >= 8X
There is a 0.1% of reference with a coverageData >= 9X
There is a 0.06% of reference with a coverageData >= 10X
There is a 0.04% of reference with a coverageData >= 11X
There is a 0.03% of reference with a coverageData >= 12X
There is a 0.02% 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% 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 88231728 0.3539879966838678 1.3777990075234798
chr2 243199373 80463560 0.3308543069311285 1.011711161019341
chr3 198022430 67077636 0.3387375662443896 0.9292793105890645
chr4 191154276 65388270 0.3420706633839569 0.892300457450574
chr5 180915260 58103700 0.3211652792583666 0.8774959827722042
chr6 171115067 61104950 0.35709859494722346 0.9407138345898284
chr7 159138663 43388205 0.27264402114525743 0.8759797808884542
chr8 146364022 48068661 0.32841855766986233 0.902132667162196
chr9 141213431 33719598 0.23878463798532024 0.8850496156901949
chr10 135534747 54697021 0.4035645634104441 1.4124390609576143
chr11 135006516 49944337 0.36994019607172146 1.0187434560073019
chr12 133851895 48114077 0.35945757062311295 0.9471738375698869
chr13 115169878 40213089 0.3491632508284849 0.9756882139682981
chr14 107349540 38486943 0.35851986883222786 0.9467854207975303
chr15 102531392 36533039 0.3563107677305308 1.0020595600110496
chr16 90354753 30275727 0.33507619682165474 1.0421065690257911
chr17 81195210 25445760 0.31338991548885703 0.9996159088029426
chr18 78077248 27878880 0.35706791304939434 1.0834562066202988
chr19 59128983 17952458 0.30361520001113496 1.15698219331422
chr20 63025520 19459972 0.3087633707742514 0.9007316021296748
chr21 48129895 13039840 0.27093015681833504 0.8492661389359318
chr22 51304566 8821974 0.17195299927105903 0.6629370790758498
chrMT 16571 480 0.028966266368957817 0.18351863529984447
chrX 155270560 22187514 0.14289582004470133 0.5910275758830106
chrY 59373566 4293724 0.07231709815105261 0.38648045223308924