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	3,882,798	T→C	D311G (GAC→GGC)	dnaA ←	chromosomal replication initiator protein DnaA, DNA‑binding transcriptional dual regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,882,798	0	T	C	96.9%	104.8 / ‑3.6	32	D311G (GAC→GGC)	dnaA	chromosomal replication initiator protein DnaA, DNA‑binding transcriptional dual regulator
Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (11/20); total (11/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.82e-01

ACGCACGAAGTCGATGGTGATCGCCCGTCCGGTAAAGTTGGCATTGGCAATGACGCGGTTCAGCGCCCCTTCCAGCTCACGTACGTTAGATCGTAGACGCTTGGCGATAAAGAACGCCACTTCGCCCGGCAAACGAATGTCGTTTTCGTCGGCCTTTTTCATCAGGATCGCCACACGGGTTTCCAGCTCTGGCGGTTCGATCGCCACAGTCAGTCCCCAACCGAAGCGGGATTTCAAACGATCCTCAACGCCGTTGATCTCTTTCGGATAGCGATCCGAGGTGAGAATGATCT  >  NC_000913/3882650‑3882942

acgcacgAAGTCGATGGTGATCGCCCGTCCGGTAAAGTTGGCATTGGCAATGACGCGGTTCAGCGCCCCTTCCAGCTCACGTACGTTAGATCGTAGACGCTTGGCGATAAAGAACGCCACTTCGCCCGGCAAACGAATGTCGTTTtcgccg                                                                                                                                                <  2:398171/151‑1 (MQ=255)

acgcacgAAGTCGATGGTGATCGCCCGTCCGGTAAAGTTGGCATTGGCAATGACGCGGTTCAGCGCCCCTTCCAGCTCACGTACGTTAGATCGTAGACGCTTGGCGATAAAGAACGCCACTTCGCCCGGCAAACGAATGTCGTTTtcgccg                                                                                                                                                >  2:251649/1‑151 (MQ=255)

  gcacgAAGTCGATGGTGATCGCCCGTCCGGTAAAGTTGGCATTGGCAATGACGCGGTTCAGCGCCCCTTCCAGCTCACGTACGTTAGATCGTAGACGCTTGGCGATAAAGAACGCCACTTCGCCCGGCAAACGAATGTCGTTTTCGCCGGc                                                                                                                                              <  1:196755/151‑1 (MQ=255)

            gATGGTGATCGCCCGTCCGGTAAAGTTGGCATTGGCAATGACGCGGTTCAGCGCCCCTTCCAGCTCACGTACGTTAGATCGTAGACGCTTGGCGATAAAGAACGCCACTTCGCCCGGCAAACGAATGTCGTTTTCGCCGGCCTTTTtcatc                                                                                                                                    >  2:144466/1‑151 (MQ=255)

            gATGGTGATCGCCCGTCCGGTAAAGTTGGCATTGGCAATGACGCGGTTCAGCGCCCCTTCCAGCTCACGTACGTTAGATCGTAGACGCTTGGCGATAAAGAACGCCACTTCGCCCGGCAAACGAATGTCGTTTTCGCCGGCCTTTTtcatc                                                                                                                                    <  1:144469/151‑1 (MQ=255)

             aTGGTGATCGCCCGTCCGGTAAAGTTGGCATTGGCAATGACGCGGTTCAGCGCCCCTTCCAGCTCACGTACGTTAGATCGTAGACGCTTGGCGATAAAGAACGCCACTTCGCCCGGCAAACGAATGTCGTTTTCGCCGGCCTTTTtcatca                                                                                                                                   <  1:633055/151‑1 (MQ=255)

                  gATCGCCCGTCCGGTAAAGTTGGCATTGGCAATGACGCGGTTCAGCGCCCCTTCCAGCTCACGTACGTTAGATCGTAGACGCTTGGCGATAAAGAACGCCACTTCGCCCGGCAAACGAATGTCGTTTTCGCCGGCCTTTTTCATCAGGAt                                                                                                                               <  1:402244/150‑1 (MQ=255)

                          gTCCGGTAAAGTTGGCATTGGCAATGACGCGGTTCAGCGCCCCTTCCAGCTCACGTACGTTAGATCGTAGACGCTTGGCGATAAAGAACGCCACTTCGCCCGGCAAACGAATGTCGTTTTCGCCGGCCTTTTTCATCAGGATCGCCACACg                                                                                                                      <  2:222852/151‑1 (MQ=255)

                                 aaaGTTGGCATTGGCAATGACGCGGTTCAGCGCCCCTTCCAGCTCACGTACGTTAGATCGTAGACGCTTGGCGATAAAGAACGCCACTTCGCCCGGCAAACGAATGTCGTTTTCGCCGGCCTTTTTCATCAGGATCGCCACACGGGTTTcc                                                                                                               <  1:185202/151‑1 (MQ=255)

                                               caATGACGCGGTTCAGCGCCCCTTCCAGCTCACGTACGTTAGATCGTAGACGCTTGGCGATAAAGAACGCCACTTCGCCCGGCAAACGAATGTCGTTTTCGCCGGCCTTTTTCATCAGGATCGCCACACGGGTTTCCAGCTCTGGCGGTTc                                                                                                 <  2:129755/151‑1 (MQ=255)

                                                   gACGCGGTTCAGCGCCCCTTCCAGCTCACGTACGTTAGATCGTAGACGCTTGGCGATAAAGAACGCCACTTCGCCCGGCAAACGAATGTCGTTTTCGCCGGCCTTTTTCATCAGGATCGCCACACGGGTTTCCAGCTCTGGCGGTTCGAt                                                                                              <  1:205259/150‑1 (MQ=255)

                                                   gACGCGGTTCAGCGCCCCTTCCAGCTCACGTACGTTAGATCGTAGACGCTTGGCGATAAAGAACGCCACTTCGCCCGGCAAACGAATGTCGTTTTCGCCGGCCTTTTTCATCAGGATCGCCACACGGGTTTCCAGCTCTGGCGGTTCGATc                                                                                             >  2:581616/1‑151 (MQ=255)

                                                    aCGCGGTTCAGCGCCCCTTCCAGCTCACGTACGTTAGATCGTAGACGCTTGGCGATAAAGAACGCCACTTCGCCCGGCAAACGAATGTCGTTTTCGCCGGCCTTTTTCATCAGGATCGCCACACGGGTTTCCAGCTCTGGCGGTTCGATCg                                                                                            <  2:210271/151‑1 (MQ=255)

                                                      gcgGTTCAGCGCCCCTTCCAGCTCACGTACGTTAGATCGTAGACGCTTGGCGATAAAGAACGCCACTTCGCCCGGCAAACGAATGTCGTTTTCGCCGGCCTTTTTCATCAGGATCGCCACACGGGTTTCCAGCTCTGGCGGTTCGATCGcc                                                                                          <  2:4231/151‑1 (MQ=255)

                                                          ttCAGCGCCCCTTCCAGCTCACGTACGTTAGATCGTAGACGCTTGGCGATAAAGAACGCCACTTCGCCCGGCAAACGAATGTCGTTTTCGCCGGCCTTTTTCATCAGGATCGCCACACGGGTTTCCAGCTCTGGCGGTTCGATCGCcac                                                                                        >  1:412509/1‑149 (MQ=255)

                                                                   ccTTCCAGCTCACGTACGTTAGATCGTAGACGCTTGGCGATAAAGAACGCCACTTCGCCCGGCAAACGAATGTCGTTTTCGCCGGCCTTTTTCATCAGGATCGCCACACGGGTTTCCAGCTCTGGCGGTTCGATCGCCACAGTCAGTcccc                                                                             >  1:244464/1‑151 (MQ=255)

                                                                    ctgccATCTCTCGTACGTTAGATCTTAGACTCTTGGCGATAAAGAACGCCACTTCGCTCGTCAAACGTTTGTCGTTTTCCTCGCCCTTTTTCATCAGGCTCGCCACACGGGTTTCCACCTCTGGCATTTCGATCGCCACAGTCAGTcccc                                                                             <  2:411519/147‑1 (MQ=255)

                                                                                 tacgtTAGATCGTAGACGCTTGGCGATAAAGAACGCCACTTCGCCCGGCAAACGAATGTCGTTTTCGCCGGCCTTTTTCATCAGGATCGCCACACGGGTTTCCAGCTCTGGCGGTTCGATCGCCACAGTCAGTCCCCAACCGAAGCGGGAt                                                               >  1:325410/1‑151 (MQ=255)

                                                                                        gATCGTAGACGCTTGGCGATAAAGAACGCCACTTCGCCCGGCAAACGAATGTCGTTTTCGCCGGCCTTTTTCATCAGGATCGCCACACGGGTTTCCAGCTCTGGCGGTTCGATCGCCACAGTCAGTCCCCAACCGAAGCGGGATTTCAAAc                                                        <  2:423616/151‑1 (MQ=255)

                                                                                                aCGCTTGGCGATAAAGAACGCCACTTCGCCCGGCAAACGAATGTCGTTTTCGCCGGCCTTTTTCATCAGGATCGCCACACGGGTTTCCAGCTCTGGCGGTTCGATCGCCACAGTCAGTCCCCAACCGAAGCGGGATTTCAAACGATCCTCa                                                <  1:510938/151‑1 (MQ=255)

                                                                                                     tGGCGATAAAGAACGCCACTTCGCCCGGCAAACGAATGTCGTTTTCGCCGGCCTTTTTCATCAGGATCGCCACACGGGTTTCCAGCTCTGGCGGTTCGATCGCCACAGTCAGTCCCCAACCGAAGCGGGATTTCAAACGATCCTCAACg                                             <  2:52345/149‑1 (MQ=255)

                                                                                                     tGGCGATAAAGAACGCCACTTCGCCCGGCAAACGAATGTCGTTTTCGCCGGCCTTTTTCATCAGGATCGCCACACGGGTTTCCAGCTCTGGCGGTTCGATCGCCACAGTCAGTCCCCAACCGAAGCGGGATTTCAAACGATCCTCAACGc                                            <  2:457409/150‑1 (MQ=255)

                                                                                                             aaGAACGCCACTTCGCCCGGCAAACGAATGTCGTTTTCGCCGGCCTTTTTCATCAGGATCGCCACACGGGTTTCCAGCTCTGGCGGTTCGATCGCCACAGTCAGTCCCCAACCGAAGCGGGATTTCAAACGATCCTCAACGCCGTTGAtct                                   >  1:267166/1‑151 (MQ=255)

                                                                                                                  cGCCACTTCGCCCGGCAAACGAATGTCGTTTTCGCCGGCCTTTTTCATCAGGATCGCCACACGGGTTTCCAGCTCTGGCGGTTCGATCGCCACAGTCAGTCCCCAACCGAAGCGGGATTTCAAACGATCCTCAACGCCGTTGATCTCTTTc                              <  2:89976/151‑1 (MQ=255)

                                                                                                                   gCCACTTCGCCCGGCAAACGAATGTCGTTTTCGCCGGCCTTTTTCATCAGGATCGCCACACGGGTTTCCAGCTCTGGCGGTTCGATCGCCACAGTCAGTCCCCAACCGAAGCGGGATTTCAAACGATCCTCAACGCCGTTGATCTCTTTCg                             >  2:380900/1‑151 (MQ=255)

                                                                                                                              cGGCAAACGAATGTCGTTTTCGCCGGCCTTTTTCATCAGGATCGCCACACGGGTTTCCAGCTCTGGCGGTTCGATCGCCACAGTCAGTCCCCAACCGAAGCGGGATTTCAAACGATCCTCAACGCCGTTGATCTCTTTCGGATAGCGATcc                  >  2:326526/1‑151 (MQ=255)

                                                                                                                                 cAAACGAATGTCGTTTTCGCCGGCCTTTTTCATCAGGATCGCCACACGGGTTTCCAGCTCTGGCGGTTCGATCGCCACAGTCAGTCCCCAACCGAAGCGGGATTTCAAACGATCCTCAACGCCGTTGATCTCTTTCGGATAGCGATCCGAg               <  2:398510/151‑1 (MQ=255)

                                                                                                                                     cGAATGTCGTTTTCGCCGGCCTTTTTCATCAGGATCGCCACACGGGTTTCCAGCTCTGGCGGTTCGATCGCCACAGTCAGTCCCCAACCGAAGCGGGATTTCAAACGATCCTCAACGCCGTTGATCTCTTTCGGATAGCGATCCGAGGTg            >  2:186318/1‑150 (MQ=255)

                                                                                                                                       aaTGTCGTTTTCGCCGGCCTTTTTCATCAGGATCGCCACACGGGTTTCCAGCTCTGGCGGTTCGATCGCCACAGTCAGTCCCCAACCGAAGCGGGATTTCAAACGATCCTCAACGCCGTTGATCTCTTTCGGATAGCGATCCGAGGTg            >  2:318162/1‑148 (MQ=255)

                                                                                                                                            cGTTTTCGCCGGCCTTTTTCATCAGGATCGCCACACGGGTTTCCAGCTCTGGCGGTTCGATCGCCACAGTCAGTCCCCAACCGAAGCGGGATTTCAAACGATCCTCAACGCCGTTGATCTCTTTCGGATAGCGATCCGAGGTGAGAATGa     <  2:202364/150‑1 (MQ=255)

                                                                                                                                            cGTTTTCGCCGGCCTTTTTCATCAGGATCGCCACACGGGTTTCCAGCTCTGGCGGTTCGATCGCCACAGTCAGTCCCCAACCGAAGCGGGATTTCAAACGATCCTCAACGCCGTTGATCTCTTTCGGATAGCGATCCGAGGTGAGAATGAt    <  1:628591/151‑1 (MQ=255)

                                                                                                                                            cGTTTTCGCCGGCCTTTTTCATCAGGATCGCCACACGGGTTTCCAGCTCTGGCGGTTCGATCGCCACAGTCAGTCCCCAACCGAAGCGGGATTTCAAACGATCCTCAACGCCGTTGATCTCTTTCGGATAGCGATCCGAGGTGAGAATGAt    <  1:326274/151‑1 (MQ=255)

                                                                                                                                              ttttCGCCGGCCTTTTTCATCAGGATCGCCACACGGGTTTCCAGCTCTGGCGGTTCGATCGCCACAGTCAGTCCCCAACCGAAGCGGGATTTCAAACGATCCTCAACGCCGTTGATCTCTTTCGGATAGCGATCCGAGGTGAGAATGATCt  >  1:456332/1‑151 (MQ=255)

                                                                                                                                               tttCGCCGGCCTTTTTCATCAGGATCGCCACACGGGTTTCCAGCTCTGGCGGTTCGATCGCCACAGTCAGTCCCCAACCGAAGCGGGATTTCAAACGATCCTCAACGCCGTTGATCTCTTTCGGATAGCGATCCGAGGTGAGAATGATCt  <  2:429559/150‑1 (MQ=255)

ACGCACGAAGTCGATGGTGATCGCCCGTCCGGTAAAGTTGGCATTGGCAATGACGCGGTTCAGCGCCCCTTCCAGCTCACGTACGTTAGATCGTAGACGCTTGGCGATAAAGAACGCCACTTCGCCCGGCAAACGAATGTCGTTTTCGTCGGCCTTTTTCATCAGGATCGCCACACGGGTTTCCAGCTCTGGCGGTTCGATCGCCACAGTCAGTCCCCAACCGAAGCGGGATTTCAAACGATCCTCAACGCCGTTGATCTCTTTCGGATAGCGATCCGAGGTGAGAATGATCT  >  NC_000913/3882650‑3882942

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `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