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 F17 I0 R2	276	45.3	3729697	93.0%	3468618	60.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	1,965,064	G→A	52.8%	I567I (ATC→ATT)	flhA ←	predicted flagellar export pore protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	1,965,064	0	G	A	52.8%	1.4 / 76.7	53	I567I (ATC→ATT)	flhA	predicted flagellar export pore protein
Reads supporting (aligned to +/- strand): ref base G (15/10); new base A (15/13); total (30/23)
Fisher's exact test for biased strand distribution p-value = 7.82e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCTGGGTAATCGCCCGTCCCAACGCCACGCGCACGACGGCGGTTAATTCATGTGGATCGCTTTGGATGGGCGCATGTTCCGCCAGCGTTTCGAGAATGGTGCGCATATCGCGAATCGGTACTTT  >  W3110S.gb/1965000‑1965123

gctgGGTAATCGCCCGTCCCAACGCCACGCGCACGACGGCGGTTAATTCATGTGGATCGCTTTGAATgg                                                         >  1:957341/1‑69 (MQ=255)

gctgGGTAATCGCCCGTCCCAACGCCACGCGCACGACGGCGGTTAATTCATGTGGATCGCTTTGAATgg                                                         >  1:1522366/1‑69 (MQ=255)

    ggTAATCGCCCGTCCCAACGCCACGCGCACGACGGCGGTTAATTCATGTGGATCGCTTAGAATGGgcg                                                      >  1:171871/1‑68 (MQ=255)

        aTCGCCCGTCCCAACGCCACGCGCACGACGGCGGTTAATTCATGTGGATCGCTTTGGATGGGCGCATGt                                                 >  1:2723189/1‑69 (MQ=255)

        aTCGCCCGTCCCAACGCCACGCGCACGACGGCGGTTAATTCATGTGGATCACTTTGGATGGGCGCATGt                                                 >  1:99327/1‑69 (MQ=255)

           gCCCGTCCCAACGCCACGCGCACGACGGCGGTTAATTCATGTGGATCGCTTTGAATGGGCGCATGTTcc                                              >  1:912324/1‑69 (MQ=255)

           gCCCGTCCCAACGCCACGCGCACGACGGCGGTTAATTCATGTGGATCGCTTTGAATGGGCGCATGTTcc                                              >  1:1494432/1‑69 (MQ=255)

           gCCCGTCCCAACGCCACGCGCACGACGGCGGTTAATTCATGTGGATCGCTTTGAATGGGCGCATGTTcc                                              >  1:46467/1‑69 (MQ=255)

           gCCCGTCCCAACGCCACGCGCACGACGGCGGTTAATTCATGTGGATCGCTTTGAATGGGCGCATGTTcc                                              >  1:1946046/1‑69 (MQ=255)

               gTCCCAACGCCACGCGCACGACGGCGGTTAATTCATGTGGATCGCTTTGGATGGGCGCATGTTCCGcc                                           <  1:469354/68‑1 (MQ=255)

                  ccAACGCCACGCGCACGTCGGCGGTTAATTCATGTGGATCGCTTTGAATGGGCGCATg                                                  <  1:1069251/58‑1 (MQ=255)

                  ccAACGCCACGCGCACGACGGCGGTTAATTCATGTGGATCGCTTTGGATGGGCGCATGTTCCGCCAGc                                        >  1:3028656/1‑68 (MQ=255)

                  ccAACGCCACGCGCACGACGGCGGTTAATTCATGTGGATCGCTTTGGATGGGCGCATGTTCCGCCAGc                                        <  1:3610206/68‑1 (MQ=255)

                  ccAACGCCACGCGCACGACGGCGGTTAATTCATGTGGATCGCTTTGGATGGGCGCATGTTCCGCCAGc                                        >  1:2281944/1‑68 (MQ=255)

                  ccAACGCCACGCGCACGACGGCGGTTAATTCATGTGGATCGCTTTGGATGGGCGCATGTTCCGCCAGCg                                       >  1:1509415/1‑69 (MQ=255)

                  ccAACGCCACGCGCACGACGGCGGTTAATTCATGTGGATCGCTTTGGATGGGCGCATGTTCCGCCAGCg                                       >  1:1295914/1‑69 (MQ=255)

                  ccAACGCCACGCGCACGACGGCGGTTAATTCATGTGGATCGCTTTGAATGGGCGCATg                                                  <  1:1111376/58‑1 (MQ=255)

                  ccAACGCCACGCGCACGACGGCGGTTAATTCATGTGGATCGCTTTGAATGGGCGCATGTTCCGCCAGCg                                       >  1:892257/1‑69 (MQ=255)

                         cACGCGCACGACGGCGGTTAATTCATGTGGATCGCTTTGGATGGGCGCATGTTCCGCCAGCGTTTCgag                                <  1:655567/69‑1 (MQ=255)

                         cACGCGCACGACGGCGGTTAATTCATGTGGATCGCTTTGGATGGGCGCATGTTCCGCCAGCGTTTCgag                                <  1:2395193/69‑1 (MQ=255)

                           cgcgCACGACGGCGGTTAATTCATGTGGATCGCTTTGAATGGGCGCATGTTCCGCCAGCGTTTCGAGaa                              <  1:1194902/69‑1 (MQ=255)

                           cgcgCACGACGGCGGTTAATTCATGTGGATCGCTTTGAATGGGCGCATGTTCCGCCAGCGTTTCGAGaa                              <  1:388352/69‑1 (MQ=255)

                            gcgcACGACGGCGGTTAATTCATGTGGATCGCTTTGAATGGGCGCATGTTCCGCCAGCGTTTCGAGAAt                             <  1:1692801/69‑1 (MQ=255)

                                           tAATTCATGTGGCTCGCTTTGAATGGGCGCATGTTCCGCCAGCGTTTCGAGAATGGTgcg                       >  1:3201324/1‑60 (MQ=255)

                                           tAATTCATGTGGATCGCTTTGGATGGGCGCATGTTCCGCCAGCGTTTCGAGAATGGTgcg                       <  1:935602/60‑1 (MQ=255)

                                           tAATTCATGTGGATCGCTTTGGATGGGCGCATGTTCCGCCAGCGTTTCGAGAATGGTgcg                       <  1:3544848/60‑1 (MQ=255)

                                           tAATTCATGTGGATCGCTTTGGATGGGCGCATGTTCCGCCAGCGTTTCGAGAATGGTgcg                       <  1:311782/60‑1 (MQ=255)

                                           tAATTCATGTGGATCGCTTTGGATGGGCGCATGTTCCGCCAGCGTTTCGAGAATGGTgcg                       <  1:1297264/60‑1 (MQ=255)

                                           tAATTCATGTGGATCGCTTTGGATGGGCGCATGTTCCGCCAGCGTTTCGAGAATGGTgcg                       >  1:2986748/1‑60 (MQ=255)

                                           tAATTCATGTGGATCGCTTTGGATGGGCGCATGTTCCGCCAGCGTTTCGAGAATGGTgcg                       <  1:1232600/60‑1 (MQ=255)

                                           tAATTCATGTGGATCGCTTTGGATGGGCGCATGTTCCGCCAGCGTTTCGAGAATGGTgcg                       >  1:266894/1‑60 (MQ=255)

                                           tAATTCATGTGGATCGCTTTGAATGGGCGCATGTTCCGCCAGCGTTTCg                                  <  1:2172626/49‑1 (MQ=255)

                                           tAATTCATGTGGATCGCTTTGAATGGGCGCATGTTCCGCCAGCGTTTCGAGAATGGTGCGCATATcgcg              >  1:133811/1‑69 (MQ=255)

                                           tAATTCATGTGGATCGCTTTGAATGGGCGCATGTTCCGACAGCGTTTCGAGAATGGTGCGCATATcgcg              >  1:3361388/1‑69 (MQ=255)

                                              ttCATGTGGATCGCTTTGGATGGGCGCATGTTCCGCCAGCGTTTCGAGAATGGTGCGCATATCGCGAAt           >  1:475537/1‑69 (MQ=255)

                                              ttCATGTGGATCGCTTTGGATGGGCGCATGTTCCGCCAGCGTTTCGAGAATGGTGCGCATATCGCGAAt           >  1:335096/1‑69 (MQ=255)

                                              ttCATGTGGATCGCTTTGGATGGGCGCATGTTCCGCCAGCGTTTCGAGAATGGTGCGCATATCGCGAAt           >  1:2568220/1‑69 (MQ=255)

                                                cATGTGGATCGCTTTGGATGGGCGCATGTTCCGCCAGCGTTTCGAGaa                              >  1:1479250/1‑48 (MQ=255)

                                                cATGTGGATCGCTTTGGATGGGCGCATGTTCCGCCAGCGTTTCGAGaa                              >  1:3374540/1‑48 (MQ=255)

                                                cATGTGGATCGCTTTGGATGGGCGCATGTTCCGCCAGCGTTTCGAGaa                              >  1:26977/1‑48 (MQ=255)

                                                cATGTGGATCGCTTAGAATGGGCGCATGTTCCGCCAGCGTTTCGAGAATGGTGCGCATATCGCGAATc          <  1:3115061/68‑1 (MQ=255)

                                                  tgtgGATCGCTTTGAATGGGCGCATGTTCCGCCAGCGTTTCGAGAATGGTGCGCATATCGCTAATCgg        <  1:478823/68‑1 (MQ=255)

                                                  tgtgGATCGCTTTGAATGGGCGCATGTTCCGCCAGCGTTTCGAGAATGGTGCGCATATCGCGAATCgg        <  1:2496638/68‑1 (MQ=255)

                                                    tgGATCGCTTTGAATGGGCGCATGTTCCGCCAGCGTTTc                                   <  1:1343233/39‑1 (MQ=255)

                                                    tgGATCGCTTTGAATGGGCGCATGTTCCGCCAGCGTTTc                                   <  1:621726/39‑1 (MQ=255)

                                                     ggATCGCTTTGGATGGGCGCATGTTCCGCCAGCGTTTCGAGAATGGTGCGCATATCGCGAATCGGTACt    >  1:1956158/1‑69 (MQ=255)

                                                      gATCGCTTTGAATGGGCGCATGTTCCGCCAGCGTTTCGAGAATGGTGCGCATATCGCGAATCGGTACt    >  1:1025034/1‑68 (MQ=255)

                                                      gATCGCTTTGAATGGGCGCATGTTCCGCCAGCGTTTCGAGAATGGTGCGCATATCGCGAATCGGTACt    <  1:1655787/68‑1 (MQ=255)

                                                      gATCGCTTTGAATGGGCGCATGTTCCGCCAGCGTTTCGAGAATGGTGCGCATATCGCGAATCGGTACt    >  1:2823312/1‑68 (MQ=255)

                                                        tCGCTTTTGATGGGCGCATGTTCCGCCAGCGTTTCGAGAATGGTGCGCATATCGCGAATCGGTACttt  <  1:3505126/68‑1 (MQ=255)

                                                        tCGCTTTGAATGGGCGCATGTTCCGCCAGCGTTTCGAGAATGGTGCGCATATcg                >  1:269271/1‑54 (MQ=255)

                                                        tCGCTTTGAATGGGCGCATGTTCCGCCAGCGTTTCGAGAATGGTGCGCATATCGCGAATCGGTACttt  <  1:61588/68‑1 (MQ=255)

                                                        tCGCTTTGAATGGGCGCATGTTCCGCCAGCGTTTCGAGAATGGTGCGCATATCGCGAATCGGTACttt  >  1:3187543/1‑68 (MQ=255)

GCTGGGTAATCGCCCGTCCCAACGCCACGCGCACGACGGCGGTTAATTCATGTGGATCGCTTTGGATGGGCGCATGTTCCGCCAGCGTTTCGAGAATGGTGCGCATATCGCGAATCGGTACTTT  >  W3110S.gb/1965000‑1965123

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A