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
A5 F1 I1 R1	770	51.4	2439994	93.8%	2288714	110.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,997,689	C→T	intergenic (‑89/+3)	insC1 ← / ← ygeQ	IS2 repressor TnpA/pseudogene, glycosyl hydrolase family 15, part of T3SS PAI ETT2 remnant

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,997,689	0	C	T	100.0%	173.7 / NA	57	intergenic (‑89/+3)	insC1/ygeQ	IS2 repressor TnpA/pseudogene, glycosyl hydrolase family 15, part of T3SS PAI ETT2 remnant
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (31/26); total (31/26)

GTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCT  >  NC_000913/2997560‑2997815

gTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGc                                                                                                                       >  1:56513/1‑139 (MQ=18)

   cGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGctct                                                                                                                    >  2:227485/1‑139 (MQ=25)

                      gCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCt                                                                                                 >  1:518034/1‑139 (MQ=255)

                          tAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGa                                                                                             <  2:360804/139‑1 (MQ=255)

                           aaGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGaa                                                                                            >  2:454250/1‑139 (MQ=255)

                                  caattaTCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGATTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGATGTTTATCTTTGaaa                                                                                           >  1:709867/1‑133 (MQ=255)

                                  caatcaTCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGaaa                                                                                           <  2:709867/133‑1 (MQ=255)

                                     tcatcTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCtt                                                                                                                   >  1:787952/1‑106 (MQ=255)

                                     tcatcTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCtt                                                                                                                   <  2:787952/106‑1 (MQ=255)

                                        tcTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTttcttc                                                                                                             <  2:1144372/109‑1 (MQ=255)

                                        tcTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTttcttc                                                                                                             >  1:1144372/1‑109 (MQ=255)

                                        tcTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGat                                                                               <  2:56513/139‑1 (MQ=255)

                                           gTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAGGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGataaa                                                                            <  1:454250/139‑1 (MQ=255)

                                            ttCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGataaat                                                                           <  2:636252/139‑1 (MQ=255)

                                               tcCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGgtgt                                                                                                       <  2:534116/108‑1 (MQ=255)

                                               tcCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGgtgt                                                                                                       >  1:534116/1‑108 (MQ=255)

                                               tcCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAAc                                                                        >  2:746409/1‑139 (MQ=255)

                                                  aaTGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACAtt                                                                     >  1:932923/1‑139 (MQ=255)

                                                      aCTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCtt                                                                                                                   >  2:833820/1‑89 (MQ=255)

                                                      aCTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCtt                                                                                                                   <  1:833820/89‑1 (MQ=255)

                                                         aGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAgg                                                                                 <  1:322462/120‑1 (MQ=255)

                                                         aGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAgg                                                                                 >  2:322462/1‑120 (MQ=255)

                                                           tCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGat                                                                               >  1:815718/1‑120 (MQ=255)

                                                           tCTAAAAACTAGTATTAAGACGATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGat                                                                               <  2:815718/120‑1 (MQ=255)

                                                               aaaaCTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCa                                                        >  2:925397/1‑139 (MQ=255)

                                                                   cTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCgg                                                    <  2:932923/139‑1 (MQ=255)

                                                                   cTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCgg                                                    <  1:746409/139‑1 (MQ=255)

                                                                    tAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGc                                                   <  2:518609/139‑1 (MQ=255)

                                                                     aGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCgg                                                    >  2:32160/1‑137 (MQ=255)

                                                                     aGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCgg                                                    <  1:32160/137‑1 (MQ=255)

                                                                     aGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCt                                                  >  1:1199195/1‑139 (MQ=255)

                                                                       tATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCt                                                  <  2:1016350/137‑1 (MQ=255)

                                                                       tATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCt                                                  >  1:1016350/1‑137 (MQ=255)

                                                                                 aTCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTctctctctgta                                      >  1:1195105/1‑132 (MQ=255)

                                                                                             aGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTcc                          >  2:243012/1‑139 (MQ=255)

                                                                                                gATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGataaa                                                                            <  2:204973/86‑1 (MQ=255)

                                                                                                gATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGataaa                                                                            >  1:204973/1‑86 (MQ=255)

                                                                                                gATATTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGa                       <  2:518034/139‑1 (MQ=255)

                                                                                                 atgttGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGAt                      <  2:1199195/136‑1 (MQ=255)

                                                                                                   atTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATaa                    >  1:448704/1‑139 (MQ=255)

                                                                                                   atTGGTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATaa                    >  1:334570/1‑139 (MQ=255)

                                                                                                      ggTTGTCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCTAGATAACCt                 >  2:191843/1‑139 (MQ=255)

                                                                                                           tCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTa                                                                                   <  2:234739/68‑1 (MQ=255)

                                                                                                           tCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTa                                                                                   >  1:234739/1‑68 (MQ=255)

                                                                                                           tCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGataaa                                                                            >  2:1044066/1‑75 (MQ=255)

                                                                                                           tCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGataaa                                                                            <  1:1044066/75‑1 (MQ=255)

                                                                                                           tCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTg                                            <  1:1037124/107‑1 (MQ=255)

                                                                                                           tCTGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTg                                            >  2:1037124/1‑107 (MQ=255)

                                                                                                             tGGAGATTCAGGGGGCCAGTTTAAACTTGCTGTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTTATGTTTATCTTTTTCCAGATAACCTGGGGAtt          <  1:243012/139‑1 (MQ=255)

                                                                                                             tGGAGATTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGAtt          >  1:1115562/1‑139 (MQ=255)

                                                                                                                agaTTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTtct                                               <  1:125277/99‑1 (MQ=255)

                                                                                                                agaTTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTtct                                               >  2:125277/1‑99 (MQ=255)

                                                                                                                  aTTCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTccc     >  1:1185428/1‑139 (MQ=255)

                                                                                                                   ttCAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTcccc    <  1:191843/139‑1 (MQ=255)

                                                                                                                     cAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTcccc    <  1:238640/137‑1 (MQ=255)

                                                                                                                     cAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTcccc    >  2:238640/1‑137 (MQ=255)

                                                                                                                     cAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCt  >  2:654794/1‑139 (MQ=255)

GTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCT  >  NC_000913/2997560‑2997815

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A