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
A3 F1 I2 R1	777	59.2	2955938	92.5%	2734242	106.9

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%	147.9 / NA	47	L118L (CTC→CTT)	flhA	putative flagellar export pore protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (27/20); total (27/20)

GAACAAAGCGCGCACCCACTTCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACGAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGTAAACAACAGAATGGT  >  NC_000913/1964582‑1964825

gaACAAAGCGCGCACCCACTTCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGac                                                                                                           <  1:1323253/139‑1 (MQ=255)

   cAAAGCGCGCACCCACTTCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGaccac                                                                                                        >  2:1124748/1‑139 (MQ=255)

     aaGCGCGCACCCACTTCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGaa                                                                                                                    >  2:207545/1‑125 (MQ=255)

     aaGCGCGCACCCACTTCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGaa                                                                                                                    <  1:207545/125‑1 (MQ=255)

                    tCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGTAAGTGACCGAACGCTTCGACCACCTTCCCTGccgccgccg                                                                                       <  2:1028054/139‑1 (MQ=255)

                        cGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCcgccgcgcc                                                                                   >  1:385310/1‑139 (MQ=255)

                         gATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCcgccgcgccg                                                                                  >  2:890222/1‑139 (MQ=255)

                                              aaTGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATg                                                             >  2:998946/1‑139 (MQ=255)

                                                 gACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGaa                                                                                                                    <  2:682782/81‑1 (MQ=255)

                                                 gACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGaa                                                                                                                    >  1:682782/1‑81 (MQ=255)

                                                 gACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTgccgccg                                                                                          <  1:327796/107‑1 (MQ=255)

                                                 gACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTgccgccg                                                                                          >  2:327796/1‑107 (MQ=255)

                                                 gACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATa                                                          >  2:546908/1‑139 (MQ=255)

                                                  aCCATAAAGTTGATGATCACGACAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATAc                                                         >  2:760138/1‑139 (MQ=255)

                                                      tAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATCGCGACCATCAAGGAAGTCACCGAACACCTCCACCACCGTCCCTGCCGCGGCCGCGCCGGTATGACCTTGCATTAAAATCAAAAGGGt                                                     >  1:25671/1‑139 (MQ=255)

                                                            tgatgaTCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGAAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGc                                               >  1:533493/1‑139 (MQ=255)

                                                              atgatCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACg                                                                                                                  <  2:1355272/70‑1 (MQ=255)

                                                              atgatCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACg                                                                                                                  >  1:1355272/1‑70 (MQ=255)

                                                                     cGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCgg                                                                                 <  1:304148/96‑1 (MQ=255)

                                                                     cGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCgg                                                                                 >  2:304148/1‑96 (MQ=255)

                                                                     cGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAg                                      >  1:1093209/1‑139 (MQ=255)

                                                                     cGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAg                                      >  2:1081930/1‑139 (MQ=255)

                                                                       agaATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTg                                    <  1:603976/139‑1 (MQ=255)

                                                                         aaTGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGATTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGcc                                  <  1:890222/139‑1 (MQ=255)

                                                                           tGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAg                                >  1:1961/1‑139 (MQ=255)

                                                                                 acacCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCaa                          <  1:998946/139‑1 (MQ=255)

                                                                                   accacGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACa                        >  1:827694/1‑139 (MQ=255)

                                                                                     cacGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGc                      >  2:5529/1‑139 (MQ=255)

                                                                                      acGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCg                     <  2:779301/139‑1 (MQ=255)

                                                                                       cGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACg                                                                                                                  >  2:1435435/1‑45 (MQ=255)

                                                                                       cGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACg                                                                                                                  <  1:1435435/45‑1 (MQ=255)

                                                                                        gATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTg                   <  2:1093209/139‑1 (MQ=255)

                                                                                          tACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGt                 >  2:631512/1‑139 (MQ=255)

                                                                                           aCCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGTa                <  1:1081930/139‑1 (MQ=255)

                                                                                             cGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGacc                                                                                                          >  2:1420174/1‑47 (MQ=255)

                                                                                             cGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGacc                                                                                                          <  1:1420174/47‑1 (MQ=255)

                                                                                             cGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTa                                                                               <  2:817918/74‑1 (MQ=255)

                                                                                             cGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTa                                                                               >  1:817918/1‑74 (MQ=255)

                                                                                                  gCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGccg                                                                          >  2:685674/1‑73 (MQ=255)

                                                                                                  gCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGccc                                                                          <  1:685674/74‑1 (MQ=255)

                                                                                                  gCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGTAAacaaca         <  2:827694/139‑1 (MQ=255)

                                                                                                   cGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCcgccgcg                                                                                     <  1:831182/62‑1 (MQ=255)

                                                                                                   cGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCcgccgcg                                                                                     >  2:831182/1‑62 (MQ=255)

                                                                                                   cGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGTa                <  2:231123/131‑1 (MQ=255)

                                                                                                   cGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGTa                >  1:231123/1‑131 (MQ=255)

                                                                                                   cGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGTAAACAACAg        >  1:817577/1‑139 (MQ=255)

                                                                                                         tGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGTAAACAACAGAATGGt  >  2:679789/1‑139 (MQ=255)

GAACAAAGCGCGCACCCACTTCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACGAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGTAAACAACAGAATGGT  >  NC_000913/1964582‑1964825

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A