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 I2 R1	760	52.7	2744488	90.2%	2475528	105.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,191,696	G→A	355 (TAG→TAA)	yqiI →	fimbrial protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,191,696	0	G	A	100.0%	149.9 / NA	47	355 (TAG→TAA)	yqiI	fimbrial protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (22/25); total (22/25)

TCTAGTGCGCCTTCGGTCACCGCACCATTCAGGGCAGAACTGAGTGCGAACCCGGCAGAAACGGTTGTTGAGGGACCGTTTAGTAAAGACGTAATCCTGAAAATCACCTATAACTAGTATCTAATACAAACACTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCTATGTTCTTCATC  >  NC_000913/3191580‑3191828

tCTAGTGCGCCTTCGGTCACCGCACCATTCAGGGCAGAACTGAGTGCGAACCCGGCAGAAACGGTTGTTGAGGGACCGTTTAGTAAAGACGTAATCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAAc                                                                                                                <  1:144645/139‑1 (MQ=255)

          cTTCGGTCACCGCACCATTCAGGGCAGAACTGAGTGCGAACCCGGCAGAAACGGTTGTTGAGGGACCGTTTAGTAAAGACGTAATCCTGAAAATCACCTATAACTAATATCTAATACa                                                                                                                           >  2:27304/1‑118 (MQ=255)

          cTTCGGTCACCGCACCATTCAGGGCAGAACTGAGTGCGAACCCGGCAGAAACGGTTGTTGAGGGACCGTTTAGTAAAGACGTAATCCTGAAAATCACCTATAACTAATATCTAATACa                                                                                                                           <  1:27304/118‑1 (MQ=255)

           ttCGGTCACCGCACCATTCAGGGCAGAACTGAGTGCGAACCCGGCAGAAACGGTTGTTGAGGGACCGTTTAGTAAAGACGTAATCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAgg                                                                                                     <  2:986711/139‑1 (MQ=255)

           ttCGGTCACCGCACCATTCAGGGCAGAACTGAGTGCGAACCCGGCAGAAACGGTTGTTGAGGGACCGTTTAGTAAAGACGTAATCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAgg                                                                                                     <  2:789115/139‑1 (MQ=255)

           ttCGGTCACCGCACCATTCAGGGCAGAACTGAGTGCGAACCCGGCAGAAACGGTTGTTGAGGGACCGTTTAGTAAAGACGTAATCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAgg                                                                                                     <  1:671921/139‑1 (MQ=255)

           ttCGGTCACCGCACCATTCAGGGCAGAACTGAGTGCGAACCCGGCAGAAACGGTTGTTGAGGGACCGTTTAGTAAAGACGTAATCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAgg                                                                                                     <  2:586769/139‑1 (MQ=255)

              ggTCACCGCACCATTCAGGGCAGAACTGAGTGCGAACCCGGCAGAAACGGTTGTTGAGGGACCGTTTAGTAAAGACGTAATCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAGGccc                                                                                                  <  1:879206/139‑1 (MQ=255)

                         cATTCAGGGCAGAACTGAGTGCGAACCCGGCAGAAACGGTTGTTGAGGGACCGTTTAGTAAAGACGTAATCCTGAAAATCACCTATAACTAATATCTAATAc                                                                                                                            <  1:444831/102‑1 (MQ=255)

                         cATTCAGGGCAGAACTGAGTGCGAACCCGGCAGAAACGGTTGTTGAGGGACCGTTTAGTAAAGACGTAATCCTGAAAATCACCTATAACTAATATCTAATAc                                                                                                                            >  2:444831/1‑102 (MQ=255)

                                 gCAGAACTGAGTGCGAACCCGGCAGAAACGGTTGTTGAGGGACCGTTTAGTAAAGACGTAATCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTAAc                                                                               <  1:1318183/139‑1 (MQ=255)

                                   aGAACTGAGTGCGAACCCGGCAGAAACGGTTGTTGAGGGACCGTTTAGTAAAGACGTAATCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTc                                                                             >  2:751913/1‑139 (MQ=255)

                                     aaCTGAGTGCGAACCCGGCAGAAACGGTTGTTGAGGGACCGTTTAGTAAAGACGTAATCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTCCa                                                                           >  1:418922/1‑139 (MQ=255)

                                          aGTGCGAACCCGGCAGAAACGGTTGTTGAGGGACCGTTTAGTAAAGACGTAATCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTCCAGctct                                                                      >  1:50401/1‑139 (MQ=255)

                                          aGTGCGAACCCGGCAGAAACGGTTGTTGAGGGACCGTTTAGTAAAGACGTAATCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTCCAGctct                                                                      <  2:418922/139‑1 (MQ=255)

                                          aGTGCGAACCCGGCAGAAACGGTTGTTGAGGGACCGTGTAGTAAAGACGTAATCCTGAAAATCACCTATAACTAATATCTAATACAAGCACTAAAACGGGCCATCAGGCCCGTTATAGCATCGCTCTAACTCCAGctct                                                                      >  2:223255/1‑139 (MQ=255)

                                               gAACCCGGCAGAAACGGTTGTTGAGGGACCGTTTAGTAAAGACGTAATCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAGGCCCGTTATATCaa                                                                                        >  2:593347/1‑115 (MQ=255)

                                               gAACCCGGCAGAAACGGTTGTTGAGGGACCGTTTAGTAAAGACGTAATCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAGGCCCGTTATATCaa                                                                                        <  1:593347/116‑2 (MQ=255)

                                                     ggCAGAAACGGTTGTTGAGGGACCGTTTAGTAAAGACGTAATCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGcat                                                           >  2:261126/1‑139 (MQ=255)

                                                                          aCCGTTTAGTAAAGACGTAATCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGc                                      <  1:751913/139‑1 (MQ=255)

                                                                            cGTTTAGTAAAGACGTAATCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCAt                                    >  2:681165/1‑139 (MQ=255)

                                                                              tttAGTAAAGACGTAATCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATaa                                  >  2:1012657/1‑139 (MQ=255)

                                                                                      aGACGTAATCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCa                          <  1:681165/139‑1 (MQ=255)

                                                                                        aCGTAATCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAgg                                                                                                     >  1:361992/1‑62 (MQ=255)

                                                                                        aCGTAATCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAgg                                                                                                     >  2:846353/1‑62 (MQ=255)

                                                                                        aCGTAATCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAgg                                                                                                     <  2:154993/62‑1 (MQ=255)

                                                                                        aCGTAATCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAgg                                                                                                     <  1:846353/62‑1 (MQ=255)

                                                                                        aCGTAATCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAgg                                                                                                     >  1:154993/1‑62 (MQ=255)

                                                                                        aCGTAATCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAgg                                                                                                     <  2:777056/62‑1 (MQ=255)

                                                                                        aCGTAATCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAgg                                                                                                     <  2:361992/62‑1 (MQ=255)

                                                                                        aCGTAATCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAgg                                                                                                     >  1:777056/1‑62 (MQ=255)

                                                                                        aCGTAATCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTaa                                                                                >  1:540827/1‑83 (MQ=255)

                                                                                        aCGTAATCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTaa                                                                                <  2:540827/83‑1 (MQ=255)

                                                                                        aCGTAATCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGc                                                                 >  1:198707/1‑98 (MQ=255)

                                                                                        aCGTAATCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGc                                                                 <  1:800903/98‑1 (MQ=255)

                                                                                        aCGTAATCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGc                                                                 <  2:198707/98‑1 (MQ=255)

                                                                                        aCGTAATCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGc                                                                 >  2:800903/1‑98 (MQ=255)

                                                                                           tAATCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAAcc                     <  2:534581/139‑1 (MQ=255)

                                                                                             aTCCTGAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAg                   >  1:955962/1‑139 (MQ=255)

                                                                                                  gAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAgg                                                                                                     >  1:1247626/1‑52 (MQ=255)

                                                                                                  gAAAATCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAgg                                                                                                     <  2:1247626/52‑1 (MQ=255)

                                                                                                   aaaaTCACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCTa             >  2:792216/1‑139 (MQ=255)

                                                                                                        cACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTCCAg                                                                          <  1:310944/73‑1 (MQ=255)

                                                                                                        cACCTATAACTAATATCTAATACAAACACTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTCCAg                                                                          >  2:310944/1‑73 (MQ=255)

                                                                                                             ataACTAATATCTAATACAAACACTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTCCAGct                                                                        >  2:1246747/1‑70 (MQ=255)

                                                                                                             ataACTAATATCTAATACAAACACTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTCCAGct                                                                        <  1:1246747/70‑1 (MQ=255)

                                                                                                              taACTAATATCTAATACAAACACTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCTCTGttcttcttc  <  1:792216/139‑1 (MQ=255)

TCTAGTGCGCCTTCGGTCACCGCACCATTCAGGGCAGAACTGAGTGCGAACCCGGCAGAAACGGTTGTTGAGGGACCGTTTAGTAAAGACGTAATCCTGAAAATCACCTATAACTAGTATCTAATACAAACACTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCTATGTTCTTCATC  >  NC_000913/3191580‑3191828

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