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
A6 F21 I0 R1	2169	63.0	3952800	76.2%	3012033	62.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	834,595	A→G	21.0%	D1018G (GAT→GGT) ‡	narG →	nitrate reductase 1, alpha subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	834,595	0	A	G	21.0%	119.4 / 29.1	62	D1018G (GAT→GGT) ‡	narG	nitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand): ref base A (28/21); new base G (4/9); total (32/30)
Fisher's exact test for biased strand distribution p-value = 1.23e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.91e-01

TCCGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGG  >  minE/834526‑834664

tCCGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGAt                                                                      >  1:2720303/1‑71 (MQ=255)

tCCGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGAt                                                                      >  1:2658065/1‑71 (MQ=255)

  cGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGa                                                                    <  1:579043/71‑1 (MQ=255)

   gCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGaa                                                                   <  1:597578/71‑1 (MQ=255)

    cTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAac                                                                  <  1:17509/71‑1 (MQ=255)

      tCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGaa                                                                   >  1:3157990/1‑68 (MQ=255)

      tCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAacac                                                                >  1:162863/1‑71 (MQ=255)

       ccGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAacac                                                                >  1:1261589/1‑70 (MQ=255)

       ccGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAacac                                                                <  1:250499/70‑1 (MQ=255)

            atatTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCt                                                          <  1:3872957/71‑1 (MQ=255)

             tatTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCtt                                                         <  1:1375015/71‑1 (MQ=255)

                 cAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTa                                                        >  1:653439/1‑68 (MQ=255)

                 cAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTa                                                        >  1:3752800/1‑68 (MQ=255)

                 cAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACa                                                      <  1:1228092/70‑1 (MQ=255)

                  cggCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTAc                                                       <  1:550323/67‑1 (MQ=255)

                  aGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAAc                                                    >  1:1431713/1‑71 (MQ=255)

                    gcgcaGCCGCGTAAAATTATCTCCAGCCCCACCTGGTCCGGTCTGGAAAGCGATCACGTCTCCTATAACg                                                   <  1:3136073/67‑1 (MQ=255)

                      acaGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGcc                                                 <  1:710114/70‑1 (MQ=255)

                      acaGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCg                                                >  1:526679/1‑71 (MQ=255)

                      acaGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCg                                                >  1:3656926/1‑71 (MQ=255)

                      acaGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCg                                                >  1:3223269/1‑71 (MQ=255)

                              gcAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGAt                                                                      >  1:715966/1‑41 (MQ=255)

                              gcAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGAt                                                                      <  1:3931577/41‑1 (MQ=255)

                              gcAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACAcc                                        <  1:1113689/71‑1 (MQ=255)

                               taaaaTTATCTCCAGCCCCACCTGGTCCGGTCTGGAAAGCGATCACGTCTCCTATAACGCggga                                              <  1:3233394/63‑2 (MQ=255)

                               cAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTacac                                         >  1:2292212/1‑69 (MQ=255)

                                aaaaTTATCTCCAGCCCGACCTGGTCTGGTCTGGATGATGAACACGTTTCTTACAACGCCGGTTACACCaa                                      >  1:1759730/1‑71 (MQ=255)

                                aaaaTTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCtt                                                         >  1:3949103/1‑52 (MQ=255)

                                 aaaTTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAAc                                     >  1:3283398/1‑71 (MQ=255)

                                 aaaTTATCTCCAGCCCCACCTGGTCCGGTCTGGAAAGCGATCACGTCTCCTATAACGCGGGATACACCAAc                                     >  1:3884871/1‑71 (MQ=255)

                                  aaTTATCTCCAGCCCGCCCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAAc                                     >  1:2240582/1‑70 (MQ=255)

                                   aTTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTa                                            >  1:3101921/1‑62 (MQ=255)

                                   aTTATCTCCAGCCCCACCTGGTCCGGTCTGGAAAGCGATCACGTCTCCTATAACGCGGGATACACCAACGt                                   <  1:2390005/71‑1 (MQ=255)

                                   aTTATCTCCAGCCCCACCTGGTCCGGTCTGGAAAGCGATCACGTCTCCTATAACGCGGGATACACCAACGt                                   <  1:2394697/71‑1 (MQ=255)

                                    ttATCTCCAGCCCCACCTGGTCCGGTCTGGAAAGCGATCACGTCTCCTATAACGCGGGATa                                            <  1:2956570/61‑1 (MQ=255)

                                    ttATCTCCAGCCCCACCTGGTCCGGTCTGGAAAGCGATCACGTCTCCTATAACGCGGGATa                                            <  1:3339452/61‑1 (MQ=255)

                                      aTCTCCAGCCCCACCTGGTCCGGTCTGGAAAGCGATCACGTCTCCTATAAc                                                    >  1:1464103/1‑51 (MQ=255)

                                       tctcCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCgg                                               >  1:49419/1‑55 (MQ=255)

                                           cAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGa                             <  1:3493738/69‑1 (MQ=255)

                                           cAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGc                           >  1:1885374/1‑71 (MQ=255)

                                            aGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCt                                                          >  1:898653/1‑39 (MQ=255)

                                               ccGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGAt                       >  1:2931444/1‑71 (MQ=255)

                                                cGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATc                      >  1:2420899/1‑71 (MQ=255)

                                                   ccTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCa                   <  1:997730/71‑1 (MQ=255)

                                                    ctggtccggtCTGGAAAGCGATCACGTCTCCTATAACGCGGGATACACCAACGTTCat                               <  1:2195101/58‑2 (MQ=255)

                                                       gtctggtctgGAAGATGAACACTTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCa                   <  1:2066342/67‑1 (MQ=255)

                                                       gtctggtctgGAAGATGAACACGTTTCTTACAACGc                                                  <  1:2911476/36‑1 (MQ=255)

                                                       gtccggtctgGAAAGCGATCACGTCTCCTATAACGCGGGATACACCAACGTTCATGAGTTAATTCCGTgg                <  1:3774248/70‑1 (MQ=255)

                                                           ggtctggAAGATTAACACGTTTCTTACAACGCCGGTTa                                            <  1:3135240/38‑1 (MQ=255)

                                                            gtctggAAAGCGATCACGTCTCCTATAACGCGGGATACACCAACGTTCATGAGTTAATTCCGTGGCGCACg          >  1:578677/1‑71 (MQ=255)

                                                            gtctggAAAGCGATCACGTCTCCTATAACGCGGGATACACCAACGTTCATGAGTTAATTCCGTGGCGCACg          >  1:1977973/1‑71 (MQ=255)

                                                             tctggAAAGCGATCACGTCTCCTATAACGCGGGATACACCAACGTTCATGAGTTAATTCCGTGGCGCACg          <  1:3428785/70‑1 (MQ=255)

                                                                 gAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGctct      <  1:1248991/70‑1 (MQ=255)

                                                                 gAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGctct      <  1:887036/70‑1 (MQ=255)

                                                                 gAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGctct      <  1:1625502/70‑1 (MQ=255)

                                                                   aGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTg   >  1:587615/1‑71 (MQ=255)

                                                                   aGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTg   >  1:1127115/1‑71 (MQ=255)

                                                                   aGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTg   >  1:1381597/1‑71 (MQ=255)

                                                                   aGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTg   >  1:3331147/1‑71 (MQ=255)

                                                                   aGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTg   >  1:3472485/1‑71 (MQ=255)

                                                                    gATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTgg  <  1:2667360/71‑1 (MQ=255)

                                                                    gATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTgg  <  1:893974/71‑1 (MQ=255)

                                                                     aTGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCa                   <  1:897873/53‑1 (MQ=255)

TCCGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGG  >  minE/834526‑834664

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A