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
A7 F28 I1 R1	183	98.6	3427438	96.9%	3321187	138.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,511,736	A→G	L324P (CTG→CCG)	mntH ←	Mn(2(+))/Fe(2(+)): H(+) symporter MntH

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,511,736	0	A	G	100.0%	143.0 / NA	39	L324P (CTG→CCG)	mntH	Mn(2(+))/Fe(2(+)): H(+) symporter MntH
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (25/14); total (25/14)

AATCAGCAGTGGAACCAGCGCCAGAGCGATACCAAAACTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCA  >  NC_000913/2511600‑2511871

aaTCAGCAGTGGAACCAGCGCCAGAGCGATACCAAAACTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACGGCg                                                                                                                                      <  2:706184/140‑1 (MQ=255)

aaTCAGCAGTGGAACCAGCGCCAGAGCGATACCAAAACTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACGGCg                                                                                                                                      <  1:1558581/140‑1 (MQ=255)

aaTCAGCAGTGGAACCAGCGCCAGAGCGATACCAAAACTTAACAGTACCTCACTCATAACTAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACGGCg                                                                                                                                      <  2:1531728/140‑1 (MQ=255)

  tCAGCAGTGGAACCAGCGCCAGAGCGATACCAAAACTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACGGCggg                                                                                                                                    <  1:218856/140‑1 (MQ=255)

            aaCCAGCGCCAGAGCGATACCAAAACTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACGGCGGGATATGAAAGc                                                                                                                          <  2:1396208/140‑1 (MQ=255)

                 gcgcCAGAGCGATACCAAAACTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACGGCGGGATATGAAAGCGAATg                                                                                                                     <  2:390338/140‑1 (MQ=255)

                 gcgcCAGAGCGATACCAAAACTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACGGCGGGATATGAAAGCGAATg                                                                                                                     <  2:1398265/140‑1 (MQ=255)

                  cgcCAGAGCGATACCAAAACTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACGGCGGGATATGAAAGCGAATGa                                                                                                                    >  2:1564169/1‑140 (MQ=255)

                   gcCAGAGCGATACCAAAACTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACGGCGGGGTATGAAAGCGAATGaa                                                                                                                   >  1:224578/1‑140 (MQ=255)

                   gcCAGAGCGATACCAAAACTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACGGCGGGATATGAAAGCGAATGaa                                                                                                                   >  1:1476137/1‑140 (MQ=255)

                      agagCGATACCAAAACTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACGGCGGGATATGAAAGCGAATGAAGcc                                                                                                                >  1:259896/1‑140 (MQ=255)

                       gagCGATACCAAAACTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACGGCGGGATATGAAAGCGAATGAAGccc                                                                                                               <  2:1436040/140‑1 (MQ=255)

                            aTACCAAAACTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACGGCGGGATATGAAAGCGAATGAAGCCCTGCAt                                                                                                          <  1:372165/140‑1 (MQ=255)

                            aTACCAAAACTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAAT‑ACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACGGCGGGATATGAAAGCGAATGAAGCCCTGCATc                                                                                                         <  1:584768/140‑1 (MQ=255)

                             tACCAAAACTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACGGCGGGATATGAAAGCGAATGAAGCCCTGCATc                                                                                                         <  1:895196/140‑1 (MQ=255)

                                 aaaaCTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACGGCGGGATATGAAAGCGAATGAAGCCCTGCATcacca                                                                                                     <  1:269633/140‑1 (MQ=255)

                                   aaCTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACGGCGGGATATGAAAGCGAATGAAGCCCTGCATCaccacc                                                                                                   >  1:963617/1‑140 (MQ=255)

                                   aaCTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACGGCGGGATATGAAAGCGAATGAAGCCCTGCATCaccacc                                                                                                   <  1:1564169/140‑1 (MQ=255)

                                        aaCAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACGGCGGGATATGAAAGCGAATGAAGccc                                                                                                               >  1:806606/1‑123 (MQ=255)

                                        aaCAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACGGCGGGATATGAAAGCGAATGAAGccc                                                                                                               <  2:806606/123‑1 (MQ=255)

                                                         aaCCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACGGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCccacca                                                                             >  1:463019/1‑140 (MQ=255)

                                                         aaCCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACGGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCccacca                                                                             >  1:596346/1‑140 (MQ=255)

                                                         aaCCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACGGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCccacca                                                                             >  1:1003402/1‑140 (MQ=255)

                                                         aaCCAAAACCCGTGTCGGATCAAACCCAAAAAGAATGAAAAAAAATGCCGCCAAAATGGTGACTGTACGACCCCCCCCCGGCGGGATATAAAAGCAAATGAAGCCCTGCACCCCCCCCTGCCCCGCCAGTGTCCccacca                                                                             <  2:292135/140‑1 (MQ=255)

                                                                         ggATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACGGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGccc                                                             >  1:697012/1‑140 (MQ=255)

                                                                                   ccAACAAAATGAAAAAAAATGACGGCAACATGGTGACTGAACGCCCCCCCCACGGCGGAATATGAAAGCAAATGAAGCCCTGCACCCCCGCCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAAcc                                                   <  2:596346/140‑1 (MQ=255)

                                                                                      tCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACGGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAgg                                                >  1:1395430/1‑140 (MQ=255)

                                                                                      tCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACGGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAgg                                                >  1:1234778/1‑140 (MQ=255)

                                                                                          aaTGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACGGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTa                                            >  1:1043928/1‑140 (MQ=255)

                                                                                                    aaTGACGGCAACATGGTGACTGTACGACGCACCCACGGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATcctgtctc                                  >  1:345994/1‑134 (MQ=255)

                                                                                                    aaTGACGGCAACATGGTGACTGTACGACGCACCCACGGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGAc                                  >  2:227432/1‑140 (MQ=255)

                                                                                                               cagggTGACTGTCCGCCGCCCCCGGGGCGGGATATAAAAGCGAATAAACCCCTGCACCCCCCCCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAg                       <  2:48772/137‑1 (MQ=255)

                                                                                                                         gTACGACGCACCCACGGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTaa             >  1:1301758/1‑140 (MQ=255)

                                                                                                                          tACGACGCACCCACGGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAAc            >  1:437904/1‑140 (MQ=255)

                                                                                                                          tACGACGCACCCACGGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAAc            >  1:1084696/1‑140 (MQ=255)

                                                                                                                              acgCACCCACGGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCg        >  2:331197/1‑140 (MQ=255)

                                                                                                                              acgCACCCACGGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCg        >  1:1643270/1‑140 (MQ=255)

                                                                                                                                gCACCCACGGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGt      >  1:37059/1‑140 (MQ=255)

                                                                                                                                  aCCCACGGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTg    >  1:455161/1‑140 (MQ=255)

                                                                                                                                    ccACGGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGcc  >  1:473997/1‑139 (MQ=255)

                                                                                                                                    ccACGGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCa  >  1:834485/1‑140 (MQ=255)

                                                                                                                                    ccACGGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCa  >  1:1083381/1‑140 (MQ=255)

AATCAGCAGTGGAACCAGCGCCAGAGCGATACCAAAACTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCA  >  NC_000913/2511600‑2511871

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A