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
A2 F50 I1 R1	170	39.5	1266514	99.2%	1256381	150.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	953,731	T→C	T246A (ACC→GCC)	focA ←	formate channel

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	953,731	0	T	C	95.1%	134.2 / ‑0.8	41	T246A (ACC→GCC)	focA	formate channel
Reads supporting (aligned to +/- strand): ref base T (1/1); new base C (18/21); total (19/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.98e-01

CTTCGACAACCATTAATGGTGGTCGTTTTCACGCAGGTAAATGACCCAGTATGTCAACCCAACCAACAAACCACCACCGATAATGTTGCCGATCGTAACCGGAATCAGGTTATCAGTGATGAAATTCATCACGGTCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAATTCCGGGGATGCGAAGTCGCGGATTACAATACCCATCGGGATCATAAACATGTTTGCGATACTGTGCTCAAAACCGCTGGCAACAAACATCGCGACCGGCA  >  NC_000913/953597‑953877

cTTCGACAACCATTAATGGTGGTCGTTTTCACGCAGGTAAATGACCCAGTATGTCAACCCAACCAACAAACCACCACCGATAATGTTGCCGATCGTAACCGGAATCAGGTTATCAGTGATGAAATTCATCACGGCCAGGTGAGAAAAAttt                                                                                                                                    >  2:142986/1‑151 (MQ=255)

   cGACAACCATTAATGGTGGTCGTTTTCACGCAGGTAAATGACCCAGTATGTCAACCCAACCAACAAACCACCACCGATAATGTTGCCGATCGTAACCGGAATCAGGTTATCAGTGATGAAATTCATCACGGCCAGGTGAGAAAAATTTTc                                                                                                                                  <  1:454133/150‑1 (MQ=255)

     aCAACCATTAATGGTGGTCGTTTTCACGCAGGTAAATGACCCAGTATGTCAACCCAACCAACAAACCACCACCGATAATGTTGCCGATCGTAACCGGAATCAGGTTATCAGTGATGAAATTCATCACGGCCAGGTGAGAAAAATTTTCCgg                                                                                                                               >  1:294954/1‑151 (MQ=255)

          cATTAATGGTGGTCGTTTTCACGCAGGTAAATGACCCAGTATGTCAACCCAACCAACAAACCACCACCGATAATGTTGCCGATCGTAACCGGAATCAGGTTATCAGTGATGAAATTCATCACGGCCAGGTGAGAAAAATTTTCCGGTGc                                                                                                                            >  2:206117/1‑149 (MQ=255)

             tAATGGTGGTCGTTTTCACGCAGGTAAATGACCCAGTATGTCAACCCAACCAACAAACCACCACCGATAATGTTGCCGATCGTAACCGGAATCAGGTTATCAGTGATGAAATTCATCACGGCCAGGTGAGAAAAATTTTCCGGTGCAGAAc                                                                                                                       >  2:11191/1‑151 (MQ=255)

                tggtggTCGTTTTCACGCAGGTAAATGACCCAGTATGTCAACCCAACCAACAAACCACCACCGATAATGTTGCCGATCGTAACCGGAATCAGGTTATCAGTGATGAAATTCATCACGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCg                                                                                                                     >  2:161997/1‑150 (MQ=255)

                     gtCGTTTTCACGCAGGTAAATGACCCAGTATGTCAACCCAACCAACAAACCACCACCGATAATGTTGCCGATCGTAACCGGAATCAGGTTATCAGTGATGAAATTCATCACGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCg                                                                                                               <  2:429945/151‑1 (MQ=255)

                               cGCAGGTAAATGACCCAGTATGTCAACCCAACCAACAAACCACCACCGATAATGTTGCCGATCGTAACCGGAATCAGGTTATCAGTGATGAAATTCATCACGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAAtt                                                                                                     >  2:404095/1‑151 (MQ=255)

                               cGCAGGTAAATGACCCAGTATGTCAACCCAACCAACAAACCACCACCGATAATGTTGCCGATCGTAACCGGAATCAGGTTATCAGTGATGAAATTCATCACGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAAtt                                                                                                     >  2:22513/1‑151 (MQ=255)

                                 cAGGTAAATGACCCAGTATGTCAACCCAACCAACAAACCACCACCGATAATGTTGCCGATCGTAACCGGAATCAGGTTATCAGTGATGAAATTCATCACGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAATTcc                                                                                                   >  1:215116/1‑151 (MQ=255)

                                        aTGACCCAGTATGTCAACCCAACCAACAAACCACCACCGATAATGTTGCCGATCGTAACCGGAATCAGGTTATCAGTGATGAAATTCATCACGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCGAAATTCCGGGGATg                                                                                            <  2:444928/151‑1 (MQ=255)

                                            cccAGTATGTCAACCCAACCAACAAACCACCACCGATAATGTTGCCGATCGTAACCGGAATCAGGTTATCAGTGATGAAATTCATCACGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAATTCCGGGGATGCGa                                                                                         >  1:3719/1‑150 (MQ=255)

                                             ccAGTATGTCAACCCAACCAACAAACCACCACCGATAATGTTGCCGATCGTAACCGGAATCAGGTTATCAGTGATGAAATTCATCACGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAATTCCGGGGATGCGa                                                                                         >  2:308290/1‑149 (MQ=255)

                                              cAGTATGTCAACCCAACCAACAAACCACCACCGATAATGTTGCCGATCGTAACCGGAATCAGGTTATCAGTGATGAAATTCATCACGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAATTCCGGGGATGCGAAGt                                                                                      <  1:255312/151‑1 (MQ=255)

                                               aGTATGTCAACCCAACCAACAAACCACCACCGATAATGTTGCCGATCGTAACCGGAATCAGGTTATCAGTGATGAAATTCATCACGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAATTCCGGGGATGCGAAGTc                                                                                     >  1:310/1‑151 (MQ=255)

                                                gTATGTCAACCCAACCAACAAACCACCACCGATAATGTTGCCGATCGTAACCGGAATCAGGTTATCAGTGATGAAATTCATCACGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAATTCCGGGGATGCGAAGTcg                                                                                    <  1:161818/151‑1 (MQ=255)

                                                    gTCAACCCAACCAACAAACCACCACCGATAATGTTGCCGATCGTAACCGGAATCAGGTTATCAGTGATGAAATTCATCACGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAATTCCGGGGATGCGAAGTCGCgg                                                                                 <  2:275181/150‑1 (MQ=255)

                                                      caacccaaccAACAAACCACCACCGATAATGTTGCCGATCGTAACCGGAATCAGGTTATCAGTGATGAAATTCATCACGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAATTCCGGGGATGCGAAGTCGCGGAtt                                                                              <  2:325742/151‑1 (MQ=255)

                                                         cccaaccAACAAACCACCACCGATAATGTTTCCGATCGTAACCGGAATCAGGTTATCAGTGATGAAATTCATCACGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAATTCCGGGGATGCGAAGTCGCGGATTAc                                                                            >  1:547718/1‑150 (MQ=255)

                                                         cccaaccAACAAACCACCACCGATAATGTTGCCGATCGTAACCGGAATCAGGTTATCAGTGATGAAATTCATCACGGTCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAATTCCGGGGATGCGAAGTCGCGGATTAc                                                                            >  2:38184/1‑150 (MQ=255)

                                                                aacaaACCACCACCGATAATGTTGCCGATCGTAACCGGAATCAGGTTATCAGTGATGAAATTCATCACGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAATTCCGGGGATGCGAAGTCGCGGATTACAATAccc                                                                     >  1:433670/1‑150 (MQ=255)

                                                                     accaccaccGATAATGTTGCCGATCGTAACCGGAATCAGGTTATCAGTGATGAAATTCATCACGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAATTCCGGGGATGCGAAGTCGCGGATTACAATACCCATCggg                                                               <  1:602950/151‑1 (MQ=255)

                                                                     accaccaccGATAATGTTGCCGATCGTAACCGGAATCAGGTTATCAGTGATGAAATTCATCACGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAATTCCGGGGATGCGAAGTCGCGGATTACAATACCCATCggg                                                               <  2:388640/151‑1 (MQ=255)

                                                                      ccaccaccGATAATGTTGCCGATCGTAACCGGAATCAGGTTATCAGTGATGAAATTCATCACGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAATTCCGGGGATGCGAAGTCGCGGATTACAATACCCATCGGGa                                                              <  1:280717/151‑1 (MQ=255)

                                                                               aTAATGTTGCCGATCGTAACCGGAATCAGGTTATCAGTGATGAAATTCATCACGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAATTCCGGGGATGCGAAGTCGCGGATTACAATACCCATCGGGATCATAAAc                                                      >  1:179952/1‑150 (MQ=255)

                                                                               aTAATGTTGCCGATCGTAACCGGAATCAGGTTATCAGTGATGAAATTCATCACGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAATTCCGGGGATGCGAAGTCGCGGATTACAATACCCATCGGGATCATAAACa                                                     <  1:601740/151‑1 (MQ=255)

                                                                                       gCCGATCGTAACCGGAATCAGGTTATCAGTGATGAAATTCATCACGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAATTCCGGGGATGCGAAGTCGCGGATTACAATACCCATCGGGATCATAAACATGTTTGc                                              <  2:262223/150‑1 (MQ=255)

                                                                                       gCCGATCGTAACCGGAATCAGGTTATCAGTGATGAAATTCATCACGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAATTCCGGGGATGCGAAGTCGCGGATTACAATACCCATCGGGATCAT‑AACATGTTTGCGa                                            <  2:264588/151‑1 (MQ=255)

                                                                                                     gAATCAGGTTATCAGTGATGAAATTCATCACGGTCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAATTCCGGGGATGCGAAGTCGCGGATTACAATACCCATCGGGATCATAAACATGTTTGCGATACTGTGCTCaaa                               <  1:38184/151‑1 (MQ=255)

                                                                                                         cAGGTTATCAGTGATGAAATTCATCACGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAATTCCGGGGTTGCGAAGTCGCGGATTACAATACCCATCGGGATCATAAACATGTTTGCGATACTGTTCTCAAAAcc                            <  1:309051/150‑1 (MQ=255)

                                                                                                         cAGGTTATCAGTGATGAAATTCATCACGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAATTCCGGGGATGCGAAGTCGCGGATTACAATACCCATCGGGATCATAAACATGTTTg                                               >  2:20113/1‑131 (MQ=255)

                                                                                                         cAGGTTATCAGTGATGAAATTCATCACGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAATTCCGGGGATGCGAAGTCGCGGATTACAATACCCATCGGGATCATAAACATGTTTg                                               <  1:20113/131‑1 (MQ=255)

                                                                                                         cAGGTTATCAGTGATGAAATTCATCACGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAATTCCGGGGATGCGAAGTCGCGGATTACAATACCCATCGGGATCATAAACATGTTTGCGATACTGTGCTCAAAACCg                           <  2:215111/151‑1 (MQ=255)

                                                                                                                  aGTGATGAAATTCATCACGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAATTCCGGGGATGCGAAGTCGCGGATTACAATACCCATCGGGATCATAAACATGTTTGCGATACTGTGCTCAAAACCGCTGGcaaca                  <  1:460814/151‑1 (MQ=255)

                                                                                                                   gTGATGAAATTCATCACGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAATTCCGGGGATGCGAAGTCGCGGATTACAATACCCATCGGGATCATAAACATGTTTGCGATACTGTGCTCAAAACCGCTGGcaaca                  >  1:466611/1‑150 (MQ=255)

                                                                                                                           aTTCATCACGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAATTCCGGGGATGCGAAGTCGCGGATTACAATACCCATCGGGATCATAAACATGTTTGCGATACTGTGCTCAAAACCGCTGGCAACAAACATcgcg         <  1:335371/151‑1 (MQ=255)

                                                                                                                             tcatcaCGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAATTCCGGGGATGCGAAGTCGCGGATTACAATACCCATCGGGATCATAAACATGTTTGCGAGACTGTGCTCAAAACCGCTGGCAACAAACATcgcgg        <  2:470933/150‑2 (MQ=255)

                                                                                                                              catcaCGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAATTCCGGGGATGCGAAGTCGCGGATTACAATACCCATCGGGATCATAAACATGTTTGCGATACTGTGCTCAAAACCGCTGGCAACAAACATCGCGAcc      >  1:444689/1‑151 (MQ=255)

                                                                                                                              catcaCGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAATTCCGGGGATGCGAAGTCGCGGATTACAATACCCATCGGGATCATAAACATGTTTGCGATACTGTGCTCAAAACCGCTGGCAACAAACATCGCGAcc      <  2:556482/151‑1 (MQ=255)

                                                                                                                                  aCGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAATTCCGGGGATGCGAAGTCGCGGATTACAATACCCATCGGGATCATAAACATGTTTGCGATACTGTGCTCAAAACCGCTGGCAACAAACATCGCGACCGgca  <  1:207551/151‑1 (MQ=255)

                                                                                                                                   cGGCCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAATTCCGGGGATGCGAAGTCGCGGATTACAATACCCATCGGGATCATAAACATGTTTGCGATACTGTGCTCAAAACCGCTGGCAACAAACATCGCGACCGgc   >  1:137848/1‑149 (MQ=255)

CTTCGACAACCATTAATGGTGGTCGTTTTCACGCAGGTAAATGACCCAGTATGTCAACCCAACCAACAAACCACCACCGATAATGTTGCCGATCGTAACCGGAATCAGGTTATCAGTGATGAAATTCATCACGGTCAGGTGAGAAAAATTTTCCGGTGCAGAACCGACTGCGGTCCAAAATTCCGGGGATGCGAAGTCGCGGATTACAATACCCATCGGGATCATAAACATGTTTGCGATACTGTGCTCAAAACCGCTGGCAACAAACATCGCGACCGGCA  >  NC_000913/953597‑953877

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A