Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A8 F380 I0 R1	15	20.3	466148	96.4%	449366	201.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	2,777,977	A→T	100%	intergenic (+195/+169)	ypjF → / ← ypjA	CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,777,977	0	A	T	100.0%	72.5 / NA	19	intergenic (+195/+169)	ypjF/ypjA	CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter
Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (10/9); total (10/9)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TCTACCGGCTTGCTAAAAACTAATGTGAAATAAACGCTTAAATACAGAGCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGACTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCAGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACAGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTCCACACCGGCACTA  >  NC_000913/2777750‑2778203

tctACCGGCTTGCTAAAAACTAATGTGAAATAAACGCTTAAATACAGAGCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGACTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAAt                                                                                                                                                                                                                          <  2:39358/238‑1 (MQ=255)

         ttGCTAAAAACTAATGTGAAATAAACGCTTAAATACAGAGCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGACTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGa                                                                                                                                                                                                                <  2:28364/239‑1 (MQ=255)

          tGCTAAAAACTAATGTGAAATAAACGCTTAAATACAGAGCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGACTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGa                                                                                                                                                                                                                <  2:224022/238‑1 (MQ=255)

                                 aCGCTTAAATACAGAGCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGACTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACaaa                                                                                                                                                                                        >  2:33721/1‑239 (MQ=255)

                                               agCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGACTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGa                                                                                                                                                                                                                >  1:216092/1‑201 (MQ=255)

                                               agCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGACTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGa                                                                                                                                                                                                                <  2:216092/201‑1 (MQ=255)

                                               agCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGACTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACa                                                                                                                                                                                    >  2:189265/1‑229 (MQ=255)

                                               agCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGACTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGa                                                                                                                                                                          >  2:8443/1‑239 (MQ=255)

                                                gCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGACTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAg                                                                                                                                                                                   <  1:189265/229‑1 (MQ=255)

                                                              aGCAAAATGCTAATCTCATAGACGAAGAGACTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGa                                                                                                                                                                                                                <  2:93715/186‑1 (MQ=255)

                                                              aGCAAAATGCTAATCTCATAGACGAAGAGACTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGa                                                                                                                                                                                                                >  1:93715/1‑186 (MQ=255)

                                                                                                                                aCATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGaaa                                                                                          >  1:200161/1‑238 (MQ=255)

                                                                                                                                                         ggACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCcg                                                                                                              >  2:201977/1‑193 (MQ=255)

                                                                                                                                                         ggACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCcg                                                                                                              <  1:201977/193‑1 (MQ=255)

                                                                                                                                                           aCCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATg                                                                                             >  1:92952/1‑208 (MQ=255)

                                                                                                                                                           aCCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATg                                                                                             <  2:92952/208‑1 (MQ=255)

                                                                                                                                                                                          tcaatTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACAGATGCGGGCTTTTTCGTTGATGGTGAGAACGAACAGTTCCAACCAGCGAcc                                >  2:75134/1‑238 (MQ=255)

                                                                                                                                                                                                            acacAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACAGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTcc              >  2:183662/1‑238 (MQ=255)

                                                                                                                                                                                                                       tCAGACTCCGCCTGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACAGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTCCACACCGGCACTa  <  1:33721/239‑1 (MQ=255)

TCTACCGGCTTGCTAAAAACTAATGTGAAATAAACGCTTAAATACAGAGCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGACTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCAGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACAGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTCCACACCGGCACTA  >  NC_000913/2777750‑2778203

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 29 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A