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
A1 F28 I1 R1	143	98.3	3330986	99.3%	3307669	138.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,302,575	T→C	Q60R (CAG→CGG)	napA ←	periplasmic nitrate reductase subunit NapA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,302,575	0	T	C	95.9%	160.2 / ‑2.4	49	Q60R (CAG→CGG)	napA	periplasmic nitrate reductase subunit NapA
Reads supporting (aligned to +/- strand): ref base T (1/1); new base C (24/23); total (25/24)
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

TTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCTGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAGAAACGGCACGGCGCTTTATCCCATTTGATGGCTTCCTGCTGACCAACAACGGCGCGGGCAACGCCCGGCACGCTGAGACCGGCAGCCGCCGCAGCGGC  >  NC_000913/2302439‑2302708

tttCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCcgcg                                                                                                                                    >  2:1611550/1‑140 (MQ=255)

tttCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCcgcg                                                                                                                                    >  2:288619/1‑140 (MQ=255)

  tCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGtt                                                                                                                                  <  1:676171/140‑1 (MQ=255)

       cGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGAc                                                                                                                             <  2:814983/140‑1 (MQ=255)

            cagcGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGaa                                                                                                                        >  1:831730/1‑140 (MQ=255)

             agcGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAAc                                                                                                                       >  1:900807/1‑140 (MQ=255)

                ggCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAAcgcc                                                                                                                    <  1:1611550/140‑1 (MQ=255)

                ggCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAAcgcc                                                                                                                    <  2:659352/140‑1 (MQ=255)

                    gCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCTGCGTTCCGACCAGAACGCCGCaa                                                                                                                >  1:1548021/1‑140 (MQ=255)

                    gCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTcc                                                                                                                                >  1:77858/1‑124 (MQ=255)

                    gCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTcc                                                                                                                                <  2:77858/124‑1 (MQ=255)

                    gCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCaa                                                                                                                >  1:601196/1‑140 (MQ=255)

                       tCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCa                                                                                                             >  2:1393133/1‑140 (MQ=255)

                        cAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAg                                                                                                            <  1:1393133/140‑1 (MQ=255)

                           aCGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAGTAc                                                                                                         >  1:305821/1‑140 (MQ=255)

                               tCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAAcgcc                                                                                                                    >  2:1392725/1‑125 (MQ=255)

                               tCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAAcgcc                                                                                                                    <  1:1392725/125‑1 (MQ=255)

                               tCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAGTACCGCa                                                                                                     >  1:1412068/1‑140 (MQ=255)

                                cTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAg                                                                                                    >  1:372307/1‑140 (MQ=255)

                                 tttACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAGa                                                                                                   >  2:830861/1‑140 (MQ=255)

                                         aCATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAGAAacggcac                                                                                           >  1:548727/1‑140 (MQ=255)

                                          cATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAGAAacggcacg                                                                                          <  2:1412068/140‑1 (MQ=255)

                                          cATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAGAAacggcacg                                                                                          <  2:900807/140‑1 (MQ=255)

                                           aTGATTTTGGGCAGGAGATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAGAAacggcacg                                                                                          >  1:1641496/1‑139 (MQ=255)

                                           aTGATTTTGGGCAGGAGATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAGAAacggcacg                                                                                          <  2:1641496/139‑1 (MQ=255)

                                               ttttGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAGAAACGGCACGGCGCt                                                                                     <  2:548727/140‑1 (MQ=255)

                                               ttttGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAGAAACGGCACGGCGCt                                                                                     <  2:372307/140‑1 (MQ=255)

                                                tttGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAGAAACGGCACGGCGCtt                                                                                    <  2:1651906/140‑1 (MQ=255)

                                                          aaaTAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAGAAacggcacgg                                                                                         >  2:680293/1‑125 (MQ=255)

                                                          aaaTAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAGAAacggcacgg                                                                                         <  1:680293/125‑1 (MQ=255)

                                                            aTAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAGAAACGGCACGGCGCTTTATCCCATTTGa                                                                        <  1:830861/140‑1 (MQ=255)

                                                                      aTGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAGAAACGGCACGGCGCTTTATCCCATTTGATGGCTTCctg                                                              <  1:144652/140‑1 (MQ=255)

                                                                      aTGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAGAAACGGCACGGCGCTTTATCCCATTTGATGGCTTCctg                                                              <  2:601196/140‑1 (MQ=255)

                                                                          aGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAGAAACGGCACGGCGCTTTAT‑CCATTTGATGGCTTCCTGCTGAc                                                         <  2:305821/140‑1 (MQ=255)

                                                                           gTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAGAAACGGCACGGCGCTTTATCCCATTTGATGGCTTCCTGCTGAc                                                         >  2:200438/1‑140 (MQ=255)

                                                                            ttCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAGAAACGGCACGGCGCTTTATCCCATTTGATGGCTTCCTGCTGAcc                                                        >  1:752396/1‑140 (MQ=255)

                                                                             tCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAGAAACGGCACGGCGCTTTATCCCATTTGATGGCTTCCTGCTGACca                                                       >  1:1565464/1‑140 (MQ=255)

                                                                              cAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAGAAACGGCACGGCGCTTTATCCCATTTGATGGCTTCCTGCTGACcaa                                                      >  1:81271/1‑140 (MQ=255)

                                                                                 gCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAGAAACGGCACGGCGCTTTATCCCATTTGATGGCTTCctgc                                                             <  2:354473/130‑1 (MQ=255)

                                                                                 gCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAGAAACGGCACGGCGCTTTATCCCATTTGATGGCTTCctgc                                                             >  1:354473/1‑130 (MQ=255)

                                                                                 gCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAGAAACGGCACGGCGCTTTATCCCATTTGATGGCTTCCTGCTGACcaacaa                                                   >  2:734693/1‑140 (MQ=255)

                                                                                     cGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACAGGTCCCTGCTGCGTTCCGACCAGAACGCCGCAATCAGTACCGCAGAAACGGCACGGCGCTTTATCCCATTTGATGGCTTCCTGCTGACCAACAACGgc                                               <  2:1548021/140‑1 (MQ=255)

                                                                                      ggTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAGAAACGGCACGGCGCTTTATCCCATTTGATGGCTTCCTGCTGACCAACAACGgcg                                              >  1:212357/1‑140 (MQ=255)

                                                                                      ggTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAGAAACGGCACGGCGCTTTATCCCATTTGATGGCTTCCTGCTGACCAACAACGgcg                                              >  2:635170/1‑140 (MQ=255)

                                                                                      ggTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAGAAACGGCACGGCGCTTTATCCCATTTGATGGCTTCCTGCTGACCAACAACGgcg                                              >  1:550096/1‑140 (MQ=255)

                                                                                           aCCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAGAAACGGCACGGCGCTTTATCCCATTTGATGGCTTCCTGCTGACCAACAACGGCGCGGGc                                         <  2:752396/140‑1 (MQ=255)

                                                                                                tGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAGAAACGGCACGGCGCTTTATCCCATTTGATGGCTTCCTGCTGACCAACAACGGCGCGGGCAACGc                                    <  2:212357/140‑1 (MQ=255)

                                                                                                  cGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAGAAACGGCACGGCGCTTTATCCCATTTGATGGCTTCCTGCTGACCAACAACGGCGCGGGCAACGccc                                  >  1:1032088/1‑140 (MQ=255)

                                                                                                           cGCCCTGACAGGCCACCACACGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAGAAACGGCACGGCGCTTTATCCCATTTGATGGCTTCCTGCTGACCAACAACGGCGCGGGCAACGCCCGGCACGCTg                         <  1:200438/140‑1 (MQ=255)

                                                                                                                             cacGTCCCTGCCGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAGAAACGGCACGGCGCTTTATCCCATTTGATGGCTTCCTGCTGACCAACAACGGCGCGGGCAACGCCCGGCACGCTGAGACCGGCAGCCGCCGCa       <  1:726784/140‑1 (MQ=255)

                                                                                                                                  cccTGCCGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAGAAACGGCACGGCGCTTTATCCCATTTGATGGCTTCCTGCTGACCAACAACGGCGCGGGCAACGCCCGGCACGCTGAGACCGGCAGCCGCCGCAGCGGc  >  1:1095638/1‑140 (MQ=255)

TTTCATACGCAGCAGCGGCTGCGTCAAACGGTCTTTACCGTACATGATTTTGGGCAGGAAATAGCCCTTAATGCAGTTCAGGCCACGGTTAACCGGTGCGTCCGGGTCGCCCTGACAGGCCACCACACGTCCCTGCTGCGTTCCGACCAGAACGCCGCAACCAGTACCGCAGAAACGGCACGGCGCTTTATCCCATTTGATGGCTTCCTGCTGACCAACAACGGCGCGGGCAACGCCCGGCACGCTGAGACCGGCAGCCGCCGCAGCGGC  >  NC_000913/2302439‑2302708

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A