BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1779214.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 = 6,850,168
number of mapped reads = 6,627,671 (96.75%)
number of supplementary alignments = 15,249 (0.22%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 3,347,914
number of mapped paired reads (second in pair) = 3,279,757
number of mapped paired reads (both in pair) = 6,549,698
number of mapped paired reads (singletons) = 77,973
number of mapped bases = 527,214,632 bp
number of sequenced bases = 527,109,809 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 47,798
duplication rate = 0.68%
>>>>>>> Insert size
mean insert size = 58,240.4673
std insert size = 2,264,526.0868
median insert size = 269
>>>>>>> Mapping quality
mean mapping quality = 52.9581
>>>>>>> ACTG content
number of A's = 162,225,085 bp (30.78%)
number of C's = 100,547,267 bp (19.08%)
number of T's = 161,791,254 bp (30.69%)
number of G's = 102,447,970 bp (19.44%)
number of N's = 98,233 bp (0.02%)
GC percentage = 38.51%
>>>>>>> Mismatches and indels
general error rate = 0.0044
number of mismatches = 2,266,092
number of insertions = 39,912
mapped reads with insertion percentage = 0.6%
number of deletions = 50,854
mapped reads with deletion percentage = 0.76%
homopolymer indels = 47.43%
>>>>>>> Coverage
mean coverageData = 0.1703X
std coverageData = 0.5404X
There is a 12.96% of reference with a coverageData >= 1X
There is a 2.84% of reference with a coverageData >= 2X
There is a 0.75% of reference with a coverageData >= 3X
There is a 0.24% of reference with a coverageData >= 4X
There is a 0.09% of reference with a coverageData >= 5X
There is a 0.04% of reference with a coverageData >= 6X
There is a 0.02% of reference with a coverageData >= 7X
There is a 0.02% of reference with a coverageData >= 8X
There is a 0.01% of reference with a coverageData >= 9X
There is a 0.01% of reference with a coverageData >= 10X
There is a 0.01% 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% of reference with a coverageData >= 14X
There is a 0% of reference with a coverageData >= 15X
There is a 0% of reference with a coverageData >= 16X
There is a 0% 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 33392932 0.13397331515575242 0.49485797253861596
chr2 243199373 45673686 0.1878034693781879 0.5163429315015412
chr3 198022430 41418676 0.2091615379126496 0.5487731963528129
chr4 191154276 43240400 0.22620681527417152 0.5681031009178344
chr5 180915260 37219797 0.20573055584144753 0.5374671378668433
chr6 171115067 25844061 0.15103322841816144 0.4672852573993226
chr7 159138663 43467724 0.27314370487076417 0.9932605908897691
chr8 146364022 42108069 0.2876941233549868 0.661346499652186
chr9 141213431 18806892 0.13318061792578356 0.45632759630372033
chr10 135534747 8712134 0.0642797082876467 0.4385250184649533
chr11 135006516 24137422 0.17878708906168647 0.5093636494987969
chr12 133851895 24717511 0.18466313831417927 0.5221085980136833
chr13 115169878 18536318 0.1609476220856985 0.4776520003276884
chr14 107349540 16249523 0.1513702154662237 0.4668221206508371
chr15 102531392 11773646 0.11482967089727993 0.40452290399866214
chr16 90354753 9033448 0.09997756288482135 0.3788484868738333
chr17 81195210 7791166 0.09595598065452383 0.36631254292026744
chr18 78077248 12934648 0.1656647529380134 0.47822615090499204
chr19 59128983 4977049 0.08417274824429163 0.3752441871433233
chr20 63025520 8544770 0.13557635065922502 0.4588559588887515
chr21 48129895 6100337 0.12674735733373196 0.4276321142966562
chr22 51304566 2598100 0.05064071685159562 0.26216791697094427
chrMT 16571 320 0.01931084424597188 0.13761517191240105
chrX 155270560 39563910 0.25480625560956305 0.6428343878729617
chrY 59373566 372093 0.006266980831166516 0.10175258821923903