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
A7 F1 I2 R1	766	64.2	3232166	90.9%	2938038	104.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,964,697	G→A	L118L (CTC→CTT)	flhA ←	putative flagellar export pore protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,964,697	0	G	A	100.0%	142.3 / NA	44	L118L (CTC→CTT)	flhA	putative flagellar export pore protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (24/20); total (24/20)

GGCATACCATCGAGAACAAAGCGCGCACCCACTTCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACGAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGTAAACAACAG  >  NC_000913/1964569‑1964819

ggCATACCATCGAGAACAAAGCGCGCACCCACTTCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGAc                                                                                                                  >  2:254395/1‑139 (MQ=255)

        aTCGAGAACAAAGCGCGCACCCACTTCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCt                                                                                                          >  1:603947/1‑139 (MQ=255)

              aaCAAAGCGCGCACCCACTTCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGacc                                                                                                    <  1:1270582/139‑1 (MQ=255)

                   aGCGCGCACCCACTTCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCtt                                                                                               >  1:651087/1‑139 (MQ=255)

                       cgcACCCACTTCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCt                                                                                           >  1:582159/1‑139 (MQ=255)

                                   tGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCcgccgcg                                                                               <  1:1406250/139‑1 (MQ=255)

                                    gCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCcgccgcgc                                                                              <  1:1457242/139‑1 (MQ=255)

                                      gATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCcgccgcgccg                                                                            <  2:651087/139‑1 (MQ=255)

                                                    cTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCAt                                                              <  2:603947/139‑1 (MQ=255)

                                                     tttGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCcgccgccgc                                                                                >  2:1321312/1‑120 (MQ=255)

                                                     tttGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCcgccgccgc                                                                                <  1:1321312/120‑1 (MQ=255)

                                                        ggTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTaaa                                                          <  1:254395/139‑1 (MQ=255)

                                                               aCCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATAc                                                   >  2:294002/1‑139 (MQ=255)

                                                                ccATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACg                                                  >  2:1295175/1‑139 (MQ=255)

                                                                 cATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACgg                                                 >  2:1596283/1‑139 (MQ=255)

                                                                  aTAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACggg                                                <  1:1256644/139‑1 (MQ=255)

                                                                        ttGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAg                                          >  2:1370743/1‑139 (MQ=255)

                                                                         tgatgaTCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGc                                         >  2:877179/1‑139 (MQ=255)

                                                                           atgatCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGac                                                                                                     <  2:677229/77‑1 (MQ=255)

                                                                           atgatCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGac                                                                                                     >  1:677229/1‑77 (MQ=255)

                                                                               tCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGtt                                   <  1:1295175/139‑1 (MQ=255)

                                                                                     gaATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGa                                                                                                                        <  1:194727/48‑1 (MQ=255)

                                                                                     gaATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGa                                                                                                                        >  2:194727/1‑48 (MQ=255)

                                                                                        tGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCcgccgcgc                                                                              >  1:1367331/1‑87 (MQ=255)

                                                                                        tGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCcgccgcgc                                                                              <  2:1367331/87‑1 (MQ=255)

                                                                                          aCAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGacc                                                                                                    >  2:976594/1‑63 (MQ=255)

                                                                                          aCAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGacc                                                                                                    <  1:976594/63‑1 (MQ=255)

                                                                                           cAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGa                                                                                                               >  2:21614/1‑51 (MQ=255)

                                                                                           cAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGa                                                                                                               <  1:21614/51‑1 (MQ=255)

                                                                                                  cacGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCtt                                                                                                         >  2:1129138/1‑50 (MQ=255)

                                                                                                  cacGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCtt                                                                                                         <  1:1129138/50‑1 (MQ=255)

                                                                                                  cacGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGc                >  1:339271/1‑139 (MQ=255)

                                                                                                    cGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATa                                                    >  2:197298/1‑101 (MQ=255)

                                                                                                    cGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATa                                                    <  1:197298/101‑1 (MQ=255)

                                                                                                    cGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGt              >  1:14636/1‑139 (MQ=255)

                                                                                                    cGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGt              >  2:791433/1‑139 (MQ=255)

                                                                                                        aCCGATAGCGAAATTGCCACCAACAAGGAAGCGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGTa          <  1:791433/139‑1 (MQ=255)

                                                                                                            aTAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCg                                                                                                       <  1:490208/42‑1 (MQ=255)

                                                                                                            aTAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCg                                                                                                       >  2:490208/1‑42 (MQ=255)

                                                                                                            aTAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCAt                                                              >  1:1144361/1‑83 (MQ=255)

                                                                                                            aTAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCAt                                                              <  2:1144361/83‑1 (MQ=255)

                                                                                                               gCGAAATTGCCACCAACAAGGAAGTGACCGAACGCt                                                                                                          <  1:316316/36‑1 (MQ=255)

                                                                                                               gCGAAATTGCCACCAACAAGGAAGTGACCGAACGCt                                                                                                          >  2:316316/1‑36 (MQ=255)

                                                                                                                cGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGTAAACAACAg  >  2:1162201/1‑139 (MQ=255)

GGCATACCATCGAGAACAAAGCGCGCACCCACTTCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACGAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGTAAACAACAG  >  NC_000913/1964569‑1964819

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A