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 F1 I1 R1	773	79.9	4112934	92.2%	3792125	104.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,842,573	C→T	157 (TAG→TAA)	hycI ←	protease involved in processing C‑terminal end of HycE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,842,573	0	C	T	100.0%	192.2 / NA	59	157 (TAG→TAA)	hycI	protease involved in processing C‑terminal end of HycE
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (31/28); total (31/28)

GCCTTATCCGGCCTACATGTCGCACGAACCATGAAGGCCCGATAAGCGCAGCGCATCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCCGACGATATCCGGCTGA  >  NC_000913/2842441‑2842705

gCCTTATCCGGCCTACATGTCGCACGAACCATGAAGGCCCGATAAGCGCAGCGCATCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTActct                                                                                                                                <  1:47950/139‑1 (MQ=255)

    tATCCGGCCTACATGTCGCACGAACCATGAAGGCCCGATAAGCGCAGCGCATCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTcttctt                                                                                                                            <  2:2013541/139‑1 (MQ=255)

          gCCTACATGTCGCACGAACCATGAAGGCCCGATAAGCGCAGCGCATCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCg                                                                                                                      >  2:1986941/1‑139 (MQ=255)

           ccTACATGTCGCACGAACCATGAAGGCCCGATAAGCGCAGCGCATCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGc                                                                                                                     >  2:1954875/1‑139 (MQ=255)

                        cGAACCATGAACGCCCGATAAGCGCAGCGCATCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAg                                                                                                        <  2:1346052/139‑1 (MQ=255)

                                gAAGGCCCGATAAGCGCAGCGCATCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCAtt                                                                                                <  2:992268/139‑1 (MQ=255)

                                 aaGGCCCGATAAGCGCAGCGCATCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCAttt                                                                                               >  1:1928539/1‑139 (MQ=255)

                                              cgcagcgcaTCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTcttctt                                                                                                                            >  1:1269378/1‑97 (MQ=255)

                                              cgcagcgcaTCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTcttctt                                                                                                                            <  2:1269378/97‑1 (MQ=255)

                                                       tCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCAttt                                                                                               <  2:1164168/117‑1 (MQ=255)

                                                       tCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCAttt                                                                                               >  1:1164168/1‑117 (MQ=255)

                                                        cGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTg                                                                        >  2:968677/1‑139 (MQ=255)

                                                          ggCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAATCGTTGAt                                                                      >  2:104854/1‑139 (MQ=255)

                                                           gCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATa                                                                     <  1:19115/139‑1 (MQ=255)

                                                             aaTTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATaaa                                                                   >  2:1417192/1‑139 (MQ=255)

                                                                     aTTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCt                                                           <  2:811122/139‑1 (MQ=255)

                                                                       ttGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTAc                                                         <  1:1954875/139‑1 (MQ=255)

                                                                         ggCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCg                                                       >  1:555860/1‑139 (MQ=255)

                                                                                    tGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATc                                            >  2:546140/1‑139 (MQ=255)

                                                                                      gTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCgg                                          <  1:1986941/139‑1 (MQ=255)

                                                                                              cATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCa                                  <  1:546140/139‑1 (MQ=255)

                                                                                                tCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCttcttc                                                                                                                           >  2:630718/1‑48 (MQ=255)

                                                                                                tCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCttcttc                                                                                                                           <  1:630718/48‑1 (MQ=255)

                                                                                                tCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTcc                                                                                                                          >  1:185421/1‑49 (MQ=255)

                                                                                                tCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTcc                                                                                                                          <  2:185421/49‑1 (MQ=255)

                                                                                                   aGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCggg                             <  2:555860/139‑1 (MQ=255)

                                                                                                      aCATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAg                                                                                      <  1:595896/79‑1 (MQ=255)

                                                                                                      aCATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAg                                                                                      >  2:595896/1‑79 (MQ=255)

                                                                                                         tCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAATCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTaa                       <  1:104854/139‑1 (MQ=255)

                                                                                                          cccTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCg                                                       <  1:375217/106‑1 (MQ=255)

                                                                                                          cccTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCg                                                       >  2:375217/1‑106 (MQ=255)

                                                                                                          cccTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTaaa                      >  2:1245647/1‑139 (MQ=255)

                                                                                                               tCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAg                    <  1:2046654/136‑1 (MQ=255)

                                                                                                               tCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAg                    >  2:2046654/1‑136 (MQ=255)

                                                                                                               tCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCcg                 >  1:704980/1‑139 (MQ=255)

                                                                                                               tCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCcg                 >  2:1365582/1‑139 (MQ=255)

                                                                                                                    aTTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATttccttcc                                                                                         <  2:1803175/62‑1 (MQ=255)

                                                                                                                    aTTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATttccttcc                                                                                         >  1:1803175/1‑62 (MQ=255)

                                                                                                                    aTTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGc                                         >  1:658803/1‑110 (MQ=255)

                                                                                                                    aTTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGc                                         <  2:658803/110‑1 (MQ=255)

                                                                                                                    aTTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCcga                <  1:548695/135‑1 (MQ=255)

                                                                                                                    aTTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCcga                >  2:548695/1‑135 (MQ=255)

                                                                                                                    aTTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCCGACGat            >  1:593469/1‑139 (MQ=255)

                                                                                                                    aTTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCCGACGat            >  2:402200/1‑139 (MQ=255)

                                                                                                                         ttAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATttccttcc                                                                                         >  1:23813/1‑57 (MQ=255)

                                                                                                                         ttAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATttccttcc                                                                                         <  2:23813/57‑1 (MQ=255)

                                                                                                                         ttAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTAcc                                                        >  2:360726/1‑90 (MQ=255)

                                                                                                                         ttAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTAcc                                                        <  1:360726/90‑1 (MQ=255)

                                                                                                                           aaTGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTc                                                                                 <  1:369067/63‑1 (MQ=255)

                                                                                                                           aaTGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTc                                                                                 >  2:369067/1‑63 (MQ=255)

                                                                                                                           aaTGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGt                                                               <  2:2027883/81‑1 (MQ=255)

                                                                                                                           aaTGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGt                                                               >  1:2027883/1‑81 (MQ=255)

                                                                                                                           aaTGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCCGACGATATCCGGc     >  1:1629139/1‑139 (MQ=255)

                                                                                                                             tGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCCGACGATATCCGGCTg   >  1:1929636/1‑139 (MQ=255)

                                                                                                                              gAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCa                                                                                       <  1:1967205/54‑1 (MQ=255)

                                                                                                                              gAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCa                                                                                       >  2:1967205/1‑54 (MQ=255)

                                                                                                                              gAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCcgacg              >  1:565039/1‑127 (MQ=255)

                                                                                                                              gAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCcgacg              <  2:565039/127‑1 (MQ=255)

                                                                                                                              gAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCCGACGATATCCGGCTGa  <  2:704980/139‑1 (MQ=255)

GCCTTATCCGGCCTACATGTCGCACGAACCATGAAGGCCCGATAAGCGCAGCGCATCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCCGACGATATCCGGCTGA  >  NC_000913/2842441‑2842705

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A