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 F1 I0 R1	4577	57.4	3436498	77.7%	2670158	63.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,426,028	A→G	44.9%	N81N (AAT→AAC)	napB ←	nitrate reductase, small, cytochrome C550 subunit, periplasmic

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,426,028	0	A	G	44.9%	10.9 / 63.9	78	N81N (AAT→AAC)	napB	nitrate reductase, small, cytochrome C550 subunit, periplasmic
Reads supporting (aligned to +/- strand): ref base A (22/21); new base G (21/14); total (43/35)
Fisher's exact test for biased strand distribution p-value = 4.97e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TAGGACTGATACGCGGCGCGCCAGTGGTGCGATAGCTTTCGACACCGTGGCACTGCAAGCAGCGATTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTGGCGGCTGATTCACAT  >  minE/1425964‑1426092

tAGGACTGATACGCGGCGCGCCAGTGGTGCGATAGCTTTCGACACCGTGGCACTGCAAGCAGCGattgg                                                              <  1:2181600/69‑1 (MQ=255)

tAGGACTGATACGCGGCGCGCCAGTGGTGCGATAGCTTTCGACACCGTGGCACTGCAAGCAGCGattgg                                                              <  1:2457594/69‑1 (MQ=255)

tAGGACTGATACGCGGCGCGCCAGTGGTGCGATAGCTTTCGACACCGTGGCACTGCAAGCAGCGattgg                                                              <  1:2775826/69‑1 (MQ=255)

tAGGACTGATACGCGGCGCGCCAGTGGTGCGATAGCTTTCGACACCGTGGCACTGCAAGCAGCGattgg                                                              <  1:128933/69‑1 (MQ=255)

  ggACTGATACGCGGCGCGCCAGTGGTGCGATAGCTTTCGACACCGTGGCACTGCAAGCAGCGattggt                                                             <  1:477959/68‑1 (MQ=255)

                  cgcCAGTGGTGCGATAGCTTTCGACACCGTGGCACTGCAAGCAGCGATTGGTATTGGTCGTTACCTGAt                                            <  1:711229/69‑1 (MQ=255)

                  cgcCAGTGGTGCGATAGCTTTCGACACCGTGGCACTGCAAGCAGCGATTGGTATTGGTCGTTACCTGAt                                            <  1:1592480/69‑1 (MQ=255)

                  cgcCAGTGGTGCGATAGCTTTCGACACCGTGGCACTGCAAGCAGCGATTGGTATTGGTCGTTACCTGAt                                            <  1:1869434/69‑1 (MQ=255)

                  cgcCAGTGGTGCGATAGCTTTCGACACCGTGGCACTGCAAGCAGCGATTGGTATTGGTCGTTACCTGAt                                            <  1:3161185/69‑1 (MQ=255)

                  cgcCAGTGGTGCGATAGCTTTCGACACCGTGGCACTGCAAGCAGCGATTGGTATTGGTCGTTACCTGAt                                            <  1:1244114/69‑1 (MQ=255)

                  cgcCAGTGGTGCGATAGCTTTCGACACCGTGGCACTGCAAGCAGCGATTGGTATTGGTCGTTACCTGAt                                            <  1:3303944/69‑1 (MQ=255)

                  cgcCAGTGGTGCGATAGCTTTCGACACCGTGGCACTGCAAGCAGCGATTGGTATTGGTCGTTACCTGAt                                            <  1:2835444/69‑1 (MQ=255)

                   gcCAGTGGTGCGATAGCTTTCGACACCGTGGCACTGCAAGCAGCGATTGGTATTGGTCGTTACCTGAt                                            <  1:1243995/68‑1 (MQ=255)

                         ggtgCGATAGCTTTCGACACCGTGGCACTGCTAGCAGCGATTGGTATTGGTCGTTACCTGATTACCTTc                                     <  1:807160/69‑1 (MQ=255)

                         ggtgCGATAGCTTTCGACACCGTGGCACTGCAAGCAGCGATTGGTATTGGTCGTTACCTGATAACCTTc                                     <  1:1327704/69‑1 (MQ=255)

                         ggtgCGATAGCTTTCGACACCGTGGCACTGCAAGCAGCGATTGGTATTGGTCGTTACCTGATAACCTTc                                     <  1:1689683/69‑1 (MQ=255)

                         ggtgCGATAGCTTTCGACACCGTGGCACTGCAAGCAGCGATTGGTATTGGTCGTTACCTGATAACCTTc                                     <  1:2347022/69‑1 (MQ=255)

                          gtgCGATAGCTTTCGACACCGTGTCACTGCAAGCAGCGATTGGTATTGGTCGTTACCTGAt                                            <  1:3436017/61‑1 (MQ=255)

                                 aGCTTTCGACACCGTGGCACTGCAAGCAGCGattggt                                                             >  1:1862431/1‑37 (MQ=255)

                                 aGCTTTCGACACCGTGGCACTGCAAGCAGCGattggt                                                             >  1:2211393/1‑37 (MQ=255)

                                 aGCTTTCGACACCGTGGCACTGCAAGCAGCGattggt                                                             >  1:2268142/1‑37 (MQ=255)

                                 aGCTTTCGACACCGTGGCACTGCAAGCAGCGattggt                                                             >  1:2987959/1‑37 (MQ=255)

                                 aGCTTTCGACACCGTGGCACTGCAAGCAGCGattggt                                                             >  1:836543/1‑37 (MQ=255)

                                 aGCTTTCGACACCGTGGCACTGCAAGCAGCGattggt                                                             >  1:566633/1‑37 (MQ=255)

                                 aGCTTTCGACACCGTGGCACTGCAAGCAGCGattggt                                                             >  1:2594297/1‑37 (MQ=255)

                                 aGCTTTCGACACCGTGGCACTGCAAGCAGCGattggt                                                             >  1:2870956/1‑37 (MQ=255)

                                 aGCTTTCGACACCGTGGCACTGCAAGCAGCGattggt                                                             >  1:1336811/1‑37 (MQ=255)

                                 aGCTTTCGACACCGTGGCACTGCAAGCAGCGattggt                                                             >  1:768422/1‑37 (MQ=255)

                                 aGCTTTCGACACCGTGGCACTGCAAGCAGCGattgg                                                              >  1:1416599/1‑36 (MQ=255)

                                 aGCTTTCGACACCGTGGCACTGCAAGCAGCGattg                                                               >  1:1420704/1‑35 (MQ=255)

                                           acCGTGGCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATaa                                          >  1:1930634/1‑46 (MQ=255)

                                           acCGTGGCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATaa                                          >  1:2975175/1‑46 (MQ=255)

                                           acCGTGGCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATaa                                          >  1:2219292/1‑46 (MQ=255)

                                           acCGTGGCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATaa                                          >  1:3149726/1‑46 (MQ=255)

                                           acCGTGGCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATaa                                          >  1:2392169/1‑46 (MQ=255)

                                           acCGTGGCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATaa                                          >  1:2561247/1‑46 (MQ=255)

                                           acCGTGGCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATaa                                          >  1:310359/1‑46 (MQ=255)

                                           acCGTGGCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATaa                                          >  1:2801278/1‑46 (MQ=255)

                                           acCGTGGCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATaa                                          >  1:2830758/1‑46 (MQ=255)

                                           acCGTGGCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATaa                                          >  1:2969656/1‑46 (MQ=255)

                                           acCGTGGCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATaa                                          >  1:1918371/1‑46 (MQ=255)

                                           acCGTGGCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATaa                                          >  1:895026/1‑46 (MQ=255)

                                           acCGTGGCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATaa                                          >  1:1215417/1‑46 (MQ=255)

                                           acCGTGGCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATaa                                          >  1:1227272/1‑46 (MQ=255)

                                           acCGTGGCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATaa                                          >  1:737840/1‑46 (MQ=255)

                                           acCGTGGCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATaa                                          >  1:1338457/1‑46 (MQ=255)

                                           acCGTGGCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATaa                                          >  1:1389937/1‑46 (MQ=255)

                                           acCGTGGCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATaa                                          >  1:593872/1‑46 (MQ=255)

                                           acCGTGGCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATaa                                          >  1:1471863/1‑46 (MQ=255)

                                           acCGTGGCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATaa                                          >  1:1632213/1‑46 (MQ=255)

                                           acCGTGGCACTGCAAGAAGCGGTTGGTATTCGTCGTTACCTGATaa                                          >  1:599878/1‑46 (MQ=38)

                                                ggCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTggcg              <  1:232061/69‑1 (MQ=255)

                                                ggCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTggcg              <  1:902124/69‑1 (MQ=255)

                                                ggCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTggcg              <  1:1918566/69‑1 (MQ=255)

                                                ggCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTggcg              <  1:1209182/69‑1 (MQ=255)

                                                ggCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTggcg              <  1:2116772/69‑1 (MQ=255)

                                                ggCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTggcg              <  1:3249421/69‑1 (MQ=255)

                                                ggCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTggcg              <  1:1871301/69‑1 (MQ=255)

                                                ggCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTggcg              <  1:3095091/69‑1 (MQ=255)

                                                ggCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTggcg              <  1:1702231/69‑1 (MQ=255)

                                                ggCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTggcg              <  1:659156/69‑1 (MQ=255)

                                                ggCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTggcg              <  1:532737/69‑1 (MQ=255)

                                                ggCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTggcg              <  1:312500/69‑1 (MQ=255)

                                                ggCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTggcg              <  1:1668762/69‑1 (MQ=255)

                                                 gCACTGCAAGCAGCGGTTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTggcg              <  1:1816646/68‑1 (MQ=255)

                                                     tGCAAGCAGCGATTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTGGCGGCTGa         <  1:3121255/69‑1 (MQ=255)

                                                     tGCAAGCAGCGATTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTGGCGGCTGa         <  1:549397/69‑1 (MQ=255)

                                                     tGCAAGCAGCGATTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTGGCGGCTGa         <  1:1076665/69‑1 (MQ=255)

                                                     tGCAAGCAGCGATTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTGGCGGCTGa         <  1:1856989/69‑1 (MQ=255)

                                                     tGCAAGCAGCGATTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTGGCGGCTGa         <  1:211948/69‑1 (MQ=255)

                                                      gCAAGCGGCGATTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTGGCGGCTGa         >  1:145927/1‑68 (MQ=255)

                                                      gCAAGCAGCGATTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCgg                         >  1:1139431/1‑52 (MQ=255)

                                                      gCAAGCAGCGATTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTGGCGGCTGa         >  1:1680582/1‑68 (MQ=255)

                                                      gCAAGCAGCGATTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTGGCGGCTGa         >  1:972848/1‑68 (MQ=255)

                                                      gCAAGCAGCGATTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTGGCGGCTGa         >  1:102912/1‑68 (MQ=255)

                                                      gCAAGCAGCGATTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTGGCGGCTGa         >  1:1539192/1‑68 (MQ=255)

                                                      gCAAGCAGCGATTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTGGCGGCTGa         >  1:2157245/1‑68 (MQ=255)

                                                      gCAAGCAGCGATTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTGGCGGCTGa         >  1:2341429/1‑68 (MQ=255)

                                                      gCAAGCAGCGATTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTGGCGGCTGa         >  1:2428796/1‑68 (MQ=255)

                                                      gCAAGCAGCGAATGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTGGCGGCTGa         >  1:122524/1‑68 (MQ=255)

                                                            agcGATTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTGGCGGCTGATTcaca   <  1:1691050/68‑1 (MQ=255)

                                                            agcGATTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTGGCGGCTGATTcaca   <  1:113159/68‑1 (MQ=255)

                                                            agcGATTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTGGCGGCTGATTcaca   <  1:1387691/68‑1 (MQ=255)

                                                            agcGATTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTGGCGGCTGATTca     >  1:1394304/1‑66 (MQ=255)

                                                            agcGATTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTGGCGGCTGATTca     >  1:2743750/1‑66 (MQ=255)

                                                            agcGATTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTGGCGGCTGATTca     >  1:2616784/1‑66 (MQ=255)

                                                            agcGATTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTGGCGGCTGATTca     >  1:1125264/1‑66 (MQ=255)

                                                            agcGATTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTGGCGGCTGATTca     >  1:1246035/1‑66 (MQ=255)

                                                            agcGATTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTGGCGGCTGATTca     >  1:678290/1‑66 (MQ=255)

                                                            agcGATTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTGGCGGCTGATTca     >  1:3218619/1‑66 (MQ=255)

                                                            agcGATTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTGGCGGCTGATTca     >  1:1423113/1‑66 (MQ=255)

                                                            agcGATTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTGGCGGCTGATTca     >  1:28996/1‑66 (MQ=255)

                                                            agcGATTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTGGCGGCTGATTca     >  1:1697220/1‑66 (MQ=255)

                                                            agcGATTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTGGCGGCTGATTca     >  1:1954618/1‑66 (MQ=255)

                                                            agcGATTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTGGCGGCTGATTCACAt  >  1:2554113/1‑69 (MQ=255)

TAGGACTGATACGCGGCGCGCCAGTGGTGCGATAGCTTTCGACACCGTGGCACTGCAAGCAGCGATTGGTATTGGTCGTTACCTGATAACCTTCAACGCTATGCGGGATCATTGGCGGCTGATTCACAT  >  minE/1425964‑1426092

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A