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
A3 F50 I2 R1	193	39.9	1341687	91.8%	1231668	149.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,357,602	A→G	F339S (TTC→TCC)	cadA ←	lysine decarboxylase, acid‑inducible

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,357,602	0	A	G	97.8%	169.5 / NA	45	F339S (TTC→TCC)	cadA	lysine decarboxylase, acid‑inducible
Reads supporting (aligned to +/- strand): ref base A (0/0); major base G (20/24); minor base T (0/1); total (20/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGTTTCTTCGTTTACGTCACCTTTAACGTGGATCATGGAAGCCTGAGAGAACGCCGCCAGCAGTTTGTGAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTTGATGAAGTCGGTGTTGTACAGCAGACCATCATAGGTAGAGTTGGTAATTACAGCATGTACCGGCCAGGTTGCGTTTGGTG  >  NC_000913/4357454‑4357743

ggTTTCTTCGTTTACGTCACCTTTAACGTGGATCATGGAAGCCTGAGAGAACGCCGCCAGCAGTTTGTGAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTgaggag                                                                                                                                             <  2:110496/151‑1 (MQ=255)

       tcGTTTACGTCACCTTTAACGTGGATCATGGAAGCCTGAGAGAACGCCGCCAGCAGTTTGTGAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGGAGTTgg                                                                                                                                         <  2:76471/148‑1 (MQ=255)

               gTCACCTTTAACGTGGATCATGGACGCCTGAGAGAACGCCGCCAGCAGTTTGTGAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCAcc                                                                                                                              >  1:661347/1‑151 (MQ=255)

                      ttAACGTGGATCATGGAAGCCTGAGAGCACGCCGCCAGCAGTTTGTGAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGAACCCACGCgg                                                                                                                       >  1:535742/1‑151 (MQ=255)

                          cGTGGATCATGGAAGCCTGAGAGAACGCCGCCAGCAGTTTGTGAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTc                                                                                                                   <  1:256552/151‑1 (MQ=255)

                             ggATCATGGAAGCCTGAGAGAACGCCGCCAGCAGTTTGTGAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCaa                                                                                                                 >  2:373375/1‑150 (MQ=255)

                               aTCATGGAAGCCTGAGAGAACGCCGCCAGCAGTTTGTGAGTGGTCTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGAGAGGAGATGGTGTAAGGCACCCACGCGGCGCCAAAGt                                                                                                              >  1:610024/1‑151 (MQ=255)

                                   tGGAAGCCTGAGAGAACGCCGCCAGCAGTTTGTGAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGtgga                                                                                                           >  1:109120/1‑150 (MQ=255)

                                        gCCTGAGAGAACGCCGCCAGCAGTTTGTGAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGAtt                                                                                                     >  2:601436/1‑151 (MQ=255)

                                                gaACGCCGCCAGCAGTTTGTGAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATcc                                                                                             >  1:426132/1‑151 (MQ=255)

                                                          agcagTTTGTGAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCt                                                                                   <  2:387794/151‑1 (MQ=255)

                                                           gcagTTTGTGAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCtt                                                                                  >  2:421907/1‑151 (MQ=255)

                                                              gTTTGTGAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTtgat                                                                               <  1:476586/151‑1 (MQ=255)

                                                              gTTTGTGAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTtgat                                                                               <  1:277097/151‑1 (MQ=255)

                                                               tttGTGAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTtgatg                                                                              >  2:68341/1‑151 (MQ=255)

                                                               tttGTGAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTtgatg                                                                              >  2:391432/1‑151 (MQ=255)

                                                                   tgAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGGTGGATTTCACATCCAGTGTTTTCTTGATGAAGt                                                                          >  2:58759/1‑151 (MQ=255)

                                                                      gTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTTGATGAAGTCgg                                                                       <  2:534565/151‑1 (MQ=255)

                                                                         gACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTTGATGAAGTCGgtgt                                                                    <  2:595667/151‑1 (MQ=255)

                                                                          aCTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGTAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTTGATGAAGTCGgtgt                                                                    <  1:102741/150‑1 (MQ=255)

                                                                                   cGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTTGATGAAGTCGGTGTTGTAcagca                                                           <  1:646336/150‑1 (MQ=255)

                                                                                     tAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTTGATGAAGTCGGTGTTGTACAGCAGAc                                                        >  1:375850/1‑151 (MQ=255)

                                                                                          cACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTTGATGAAGTCGGTGTTGTACAGCAGACcatc                                                    >  2:24047/1‑150 (MQ=255)

                                                                                                cccTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTTGATGAAGTCGGTGTTGTACAGCAGACCATCATAGGt                                              <  2:71325/150‑1 (MQ=255)

                                                                                                      tACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTTGATGAAGTCGGTGTTGTACAGCAGACCATCATAGGTAGAGTTg                                       >  2:381389/1‑151 (MQ=255)

                                                                                                       acacGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTTGATGAAGTCGGTGTTGTACAGCAGACCATCATAGGTAGAGtt                                        <  1:41162/149‑1 (MQ=255)

                                                                                                       acacGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTTGATGAAGTCGGTGTTGTACAGCAGACCATCATAGGTAGAGt                                         <  2:624291/148‑1 (MQ=255)

                                                                                                         acGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTTGATGAAGTCGGTGTTGTACAGCAGACCATCATAGGTAGAGTTGGTa                                    <  1:269379/151‑1 (MQ=255)

                                                                                                         acGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTTGATGAAGTCGGTGTTGTACAGCAGACCATCATAGGTAGAGTTGGTa                                    <  2:425086/151‑1 (MQ=255)

                                                                                                          cGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTTGATGAAGTCGGTGTTGTACAGCAGACCATCATAGGTAGAGTTGGTaa                                   <  1:102165/151‑1 (MQ=255)

                                                                                                              cACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTTGATGAAGTCGGTGTTGTACAGCAGACCATCATAGGTAGAGTTGGTAATTAc                               <  2:253678/151‑1 (MQ=255)

                                                                                                              cACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTTGATGAAGTCGGTGTTGTACAGCAGACCATCATAGGTAGAGTTGGTAATTAc                               <  1:381385/151‑1 (MQ=255)

                                                                                                                  gCTCATACCGCATTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTTGATGAAGTCGGTGTTGTACAGCAGACCATCATAGGTAGAGTTGGTAATTACAGCa                           <  1:615955/151‑1 (MQ=255)

                                                                                                                     cATACCGCATTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTTGATGAAGTCGGTGTTGTACAGCAGACCATCATAGGTAGAGTTGGTAATTACAGCAt                          <  1:8435/149‑1 (MQ=255)

                                                                                                                       tACCGCATTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTTGATGaa                                                                            <  2:358866/97‑1 (MQ=255)

                                                                                                                       tACCGCATTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTTGATGaa                                                                            >  1:358862/1‑97 (MQ=255)

                                                                                                                        aCCGCATTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTTGATGAAGTCGGTGTTGTACAGCAGACCATCATAGGTAGAGTTGGTAATTACAGCATGTAc                      <  1:649667/150‑1 (MQ=255)

                                                                                                                             aTTTACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTTGATGAAGTCGGTGTTGTACAGCAGACCATCATAGGTAGAGTTGGTAATTACAGCATGTACCGGCCa                <  2:313618/151‑1 (MQ=255)

                                                                                                                              tttACCTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGACGGATTTCACATCCAGTGTTTTCTTGATGAAGTCGGTGTTGTACAGCAGACCATCATAGGTAGAGTTGGTAATTACAGCATGTACCGGcc                 >  1:479018/1‑149 (MQ=255)

                                                                                                                                  ccTTCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTTGATGAAGTCGGTGTTGTACAGCAGACCATCATAGGTAGAGTTGGTAATTACAGCATGTACCGGCCAGGTTg           >  1:242144/1‑151 (MQ=255)

                                                                                                                                     tCGTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTTGATGAAGTCGGTGTTGTACAGCAGACCATCATAGGTAGAGTTGGTAATTACAGCATGTACCGGCCAGGTTGCg         <  2:242145/150‑1 (MQ=255)

                                                                                                                                       gTAAATCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTTGATGAAGTCGGTGTTGTACAGCAGACCATCATAGGTAGAGTTGGTAATTACAGCATGTACCGGCCAGGTTGCGttt      >  2:526345/1‑151 (MQ=255)

                                                                                                                                         aaaTCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTTGATGAAGTCGGTGTTGTACAGCAGACCATCATAGGTAGAGTTGGTAATTACAGCATGTACCGGCCAGGTTGCGTTTgg    >  2:553967/1‑151 (MQ=255)

                                                                                                                                           aTCGGTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTTGATGAAGTCGGTGTTGTACAGCAGACCATCATAGGTAGAGTTGGTAATTACAGCATGTACCGGCCAGGTTGCGTTTGgtg  <  1:494293/151‑1 (MQ=255)

                                                                                                                                               gTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTTGATGAAGTCGGTGTTGTACAGCAGACCATCATAGGTAGAGTTGGTAATTACAGCATGTACCGGCCAGGTTGCGt        >  1:62133/1‑141 (MQ=255)

                                                                                                                                               gTGAGGAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTTGATGAAGTCGGTGTTGTACAGCAGACCATCATAGGTAGAGTTGGTAATTACAGCATGTACCGGCCAGGTTGCGt        <  2:62132/141‑1 (MQ=255)

GGTTTCTTCGTTTACGTCACCTTTAACGTGGATCATGGAAGCCTGAGAGAACGCCGCCAGCAGTTTGTGAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCAGTGTTTTCTTGATGAAGTCGGTGTTGTACAGCAGACCATCATAGGTAGAGTTGGTAATTACAGCATGTACCGGCCAGGTTGCGTTTGGTG  >  NC_000913/4357454‑4357743

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 18 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A