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
A9 F1 I1 R1	64	69.7	3300380	93.4%	3082554	111.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,672,123	G→A	G26E (GGG→GAG)	hcaD →	phenylpropionate dioxygenase, ferredoxin reductase subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,672,123	0	G	A	100.0%	181.1 / NA	52	G26E (GGG→GAG)	hcaD	phenylpropionate dioxygenase, ferredoxin reductase subunit
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (26/26); total (26/26)

AGCGATTCGCGGCATTCGCCACGTAGCGGCTGGGCTGGATCTTTAAGGAAGCACGATGAAAGAAAAAACGATCATTATTGTCGGTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGGGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGACATCTTCCTTATGAACGACCTCCACTCTCGAAATCCATGTTGCTGGAAGATTCCCCGCAGTTACAGCAGGTGTTACCCGCTAACTGGTGGCAGGAA  >  NC_000913/2671992‑2672256

aGCGATTCGCGGCATTCGCCACGTAGCGGCTGGGCTGGATCTTTAAGGAAGCACGATGAAAGAAAAAACGATCATTATTGTCGGTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCAcc                                                                                                                                >  2:1526643/1‑139 (MQ=255)

    aTTCGCGGCATTCGCCACGTAGCGGCTGGGCTGGATCTTTAAGGAAGCACGATGAAAGAAAAAACGATCATTATTGTCGGTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTg                                                                                                                            <  2:1492614/139‑1 (MQ=255)

      tCGCGGCATTCGCCACGTAGCGGCTGGGCTGGATCTTTAAGGAAGCACGATGAAAGAAAAAACGATCATTATTGTCGGTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAg                                                                                                                          >  2:77790/1‑139 (MQ=255)

                      gTAGCGGCTGGGCTGGATCTTTAAGGAAGCACGATGAAAGAAAAAACGATCATTATTGTCGGTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCg                                                                                                          <  1:39881/139‑1 (MQ=255)

                           ggctgggctgGATCTTTAAGGAAGCACGATGAAAGAAAAAACGATCATTATTGTCGGTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAg                                                                                                     >  2:1446697/1‑139 (MQ=255)

                                ggctggATCTTTAAGGAAGCACGATGAAAGAAAAAACGATCATTATTGTCGGTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGACa                                                                                                >  1:1389429/1‑139 (MQ=255)

                                ggctggATCTTTAAGGAAGCACGATGAAAGAAAAAACGATCATTATTGTCGGTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGACGAGCGACa                                                                                                >  2:978509/1‑139 (MQ=255)

                                  ctggATCTTTAAGGAAGCACGATGAAAGAAAAAACGATCATTATTGTCGGTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGACATc                                                                                              <  2:47794/139‑1 (MQ=255)

                                  ctggATCTTTAAGGAAGCACGATGAAAGAAAAAACGATCATTATTGTCGGTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGACATc                                                                                              <  2:1536132/139‑1 (MQ=255)

                                   tggATCTTTAAGGAAGCACGATGAAAGAAAAAACGATCATTATTGTCGGTGGCGGGCAAGCGGCGACAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGACATCt                                                                                             <  1:1186833/139‑1 (MQ=255)

                                             aGGAAGCACGATGAAAGAAAAAACGATCATTATTGTCGGTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGACATCTTCCTTATGaa                                                                                   <  2:1389429/139‑1 (MQ=255)

                                                  gCACGATGAAAGAAAAAACGATCATTATTGTCGGTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGc                                                                                                    <  2:519127/117‑1 (MQ=255)

                                                  gCACGATGAAAGAAAAAACGATCATTATTGTCGGTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGc                                                                                                    >  1:519127/1‑117 (MQ=255)

                                                   cACGATGAAAGAAAAAACGATCATTATTGTCGGTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGACATCTTCCTTAt                                                                                      <  1:807655/130‑1 (MQ=255)

                                                   cACGATGAAAGAAAAAACGATCATTATTGTCGGTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGACATCTTCCTTAt                                                                                      >  2:807655/1‑130 (MQ=255)

                                                   cACGATGAAAGAAAAAACGATCATTATTGTCGGTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGACATCTTCCTTATGAACGAcgt                                                                             >  1:967784/1‑137 (MQ=255)

                                                   cACGATGAAAGAAAAAACGATCATTATTGTCGGTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGACATCTTCCTTATGAACGACCt                                                                             >  2:1308660/1‑139 (MQ=255)

                                                       aTGAAAGAAAAAACGATCATTATTGTCGGTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGACATCTTCCTTATGAACGACCTCCAc                                                                         <  1:1470909/139‑1 (MQ=255)

                                                              aaaaaaCGATCATTATTGTCGGTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGACATCTTCCTTATGAACGACCTCCACTCTCGaa                                                                  <  1:1644327/139‑1 (MQ=255)

                                                                  aaCGATCATTATTGTCGGTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGa                                                                                                  <  2:833603/103‑1 (MQ=255)

                                                                  aaCGATCATTATTGTCGGTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGa                                                                                                  >  1:833603/1‑103 (MQ=255)

                                                                   aCGATCATTATTGTCGGTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGACATCTTCCTTATGAACGACCACCACTCTCGAAATCCa                                                             <  1:506288/139‑1 (MQ=255)

                                                                      aTCATTATTGTCGGTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGACATCTTCCTTATGAACGACCTCCACTCTCGAAATCCATGt                                                          <  1:1308660/139‑1 (MQ=255)

                                                                               gTCGGTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAg                                                                                                                          <  1:1250611/66‑1 (MQ=255)

                                                                               gTCGGTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAg                                                                                                                          >  2:1250611/1‑66 (MQ=255)

                                                                                  ggTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGACATCTTCCTTATGaa                                                                                   >  1:964879/1‑102 (MQ=255)

                                                                                  ggTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGACATCTTCCTTATGaa                                                                                   <  2:964879/102‑1 (MQ=255)

                                                                                  ggTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGACATCTTCCTTATGAACGACCTCCACTCTCGAAATCCAt                                                            <  1:213099/125‑1 (MQ=255)

                                                                                  ggTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGACATCTTCCTTATGAACGACCTCCACTCTCGAAATCCAt                                                            >  2:213099/1‑125 (MQ=255)

                                                                                  ggTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGACATCTTCCTTATGAACGACCTCCACTCTCGAAATCCATGTTGCTGGAAGAtt                                              >  2:920347/1‑139 (MQ=255)

                                                                                  ggTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGACATCTTCCTTATGAACGACCTCCACTCTCGAAATCCATGTTGCTGGAAGAtt                                              >  2:310620/1‑139 (MQ=255)

                                                                                  ggTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGACATCTTCCTTATGAACGACCTCCACTCTCGAAATCCATGTTGCTGGAAGAtt                                              >  1:269077/1‑139 (MQ=255)

                                                                                  ggTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGACATCTTCCTTATGAACGACCTCCACTCTCGAAATCCATGTTGCTGGAAGAtt                                              >  1:1472760/1‑139 (MQ=255)

                                                                                   gTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGtt                                                                                                                                    >  1:439569/1‑52 (MQ=255)

                                                                                   gTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGtt                                                                                                                                    <  2:439569/52‑1 (MQ=255)

                                                                                     ggCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGACATCTTCCTTATGAACGACCTCCACTCTCGAAATCCATGTTGCTGGAAGATTccc                                           >  2:606889/1‑139 (MQ=255)

                                                                                       cGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCAt                                                                                                                    <  1:1219960/64‑1 (MQ=255)

                                                                                       cGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCAt                                                                                                                    >  2:1219960/1‑64 (MQ=255)

                                                                                         ggCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGAt                                                                                                        <  2:843319/74‑1 (MQ=255)

                                                                                         ggCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGAt                                                                                                        >  1:843319/1‑74 (MQ=255)

                                                                                         ggCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGTCATCTTCCTTATGAACGACCTCCACTCTCGAAATCCATGTTGCTGGAAGAGTCCCCGCa                                       >  1:1000765/1‑139 (MQ=255)

                                                                                          gCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGACATCTTCCTTATGAACGACCTCCACTCTCGAAATCCATGTTGCTGGAAGATTCCCCGCAg                                      >  2:58323/1‑139 (MQ=255)

                                                                                             aGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCa                                                                                                                                  <  2:409765/44‑1 (MQ=255)

                                                                                             aGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCa                                                                                                                                  >  1:409765/1‑44 (MQ=255)

                                                                                                ggcggcAATGGCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGACATCTTCCTTATGAACGACCTCCACTCTCGAAATCCATGTTGCTGGAAGATTCCCCGCAGTTAcag                                <  1:606889/139‑1 (MQ=255)

                                                                                                          gCTGCGGCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGACATCTTCCTTATGAACGACCTCCACTCTCGAAATCCATGTTGCTGGAAGATTCCCCGCAGTTACAGCAGGTGTTAc                      <  1:920347/139‑1 (MQ=255)

                                                                                                               ggCCTCGCTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGACATCTTCCTTATGAACGACCTCCACTCTCGAAATCCATGTTGCTGGAAGATTCCCCGCAGTTACAGCAGGTGTTACCCGCt                 <  1:58323/139‑1 (MQ=255)

                                                                                                                      cTACGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGACATCTTCCTTATGAACGACCTCCACTCTCGAAATCCATGTTGCTGGAAGATTCCCCGCAGTTACAGCAGGTGTTACCCGCTAACtggt          <  2:1548516/139‑1 (MQ=255)

                                                                                                                        aCGCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGACATCTTCCTTATGAACGACCTCCACTCTCGAAATCCATGTTGCTGGAAGATTCCCCGCAGTTACAGCAGGTGTTACCCGCTAACtggtgg        <  2:1472760/139‑1 (MQ=255)

                                                                                                                          gCCAGCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGACATCTTCCTTATGAACGACCTCCACTCTCGAAATCCATGTTGCTGGAAGATTCCCCGCAGTTACAGCAGGTGTTACCCGCTAACTGGTGGCa      >  2:17382/1‑139 (MQ=255)

                                                                                                                              gCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGACATCTTCCTTATGAACGACCTCCACTCTCGAAATCCATGTTGCTGGAAGATTCCCCGCAGTTACAGCAGGTGTTACCCGCTAACTGGTGGCAGGaa  >  2:228440/1‑139 (MQ=255)

                                                                                                                              gCAAGAGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGACATCTTCCTTATGAACGACCTCCACTCTCGAAATCCATGTTGCTGGAAGATTCCCCGCAGTTACAGCAGGTGTTACCCGCTAACTGGTGGCAGGaa  <  1:1446697/139‑1 (MQ=255)

AGCGATTCGCGGCATTCGCCACGTAGCGGCTGGGCTGGATCTTTAAGGAAGCACGATGAAAGAAAAAACGATCATTATTGTCGGTGGCGGGCAAGCGGCGGCAATGGCTGCGGCCTCGCTACGCCAGCAAGGGTTCACCGGTGAGCTGCATCTGTTTTCCGATGAGCGACATCTTCCTTATGAACGACCTCCACTCTCGAAATCCATGTTGCTGGAAGATTCCCCGCAGTTACAGCAGGTGTTACCCGCTAACTGGTGGCAGGAA  >  NC_000913/2671992‑2672256

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 31 ≤` `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