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
A14 F1 I2 R1	774	49.2	2112398	96.9%	2046913	118.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,673,768	G→A	141 (TAG→TAA)	yphA →	DoxX family inner membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,673,768	0	G	A	100.0%	163.7 / NA	51	141 (TAG→TAA)	yphA	DoxX family inner membrane protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (24/27); total (24/27)

ACCATTACTGGGATATGACCGGCGATGCGGTTGGGCCAAATATGATTAATTTCTGGAAGAATGTCAGTATCGCTGGCGCGTTCTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAGGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGCATTTAATAAATTACAGCCACTCTACCCGCAACGACATCTCTGAAGTTGTTGATTCCCCTGGTGCTAGCGCAATGAGATCACCCCCTTCCGGGCGA  >  NC_000913/2673635‑2673900

aCCATTACTGGGATATGACCGGCGATGCGGTTGGGCCAAATATGATTAATTTCTGGAAGAATGTCAGTATCGCTGGCGCGTTCTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAg                                                                                                                                 <  1:42007/139‑1 (MQ=255)

  cATTACTGGGATATGACCGGCGATGCGGTTGGGCCAAATATGATTAATTTCTGGAAGAATGTCAGTATCGCTGGCGCGTTCTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAGAt                                                                                                                               >  2:478009/1‑139 (MQ=255)

        tGGGATATGACCGGCGATGCGGTTGGGCCAAATATGATTAATTTCTGGAAGAATGTCAGTATCGCTGGCGCGTTCTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGa                                                                                                                         >  1:337574/1‑139 (MQ=255)

          ggATATGACCGGCGATGCGGTTGGGCCAAATATGATTAATTTCTGGAAGAATGTCAGTATCGCTGGCGCGTTCTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATg                                                                                                                       >  1:898708/1‑139 (MQ=255)

            atatGACCGGCGATGCGGTTGGGCCAAATATGATTAATTTCTGGAAGAATGTCAGTATCGCTGGCGCGTTCTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATgcg                                                                                                                     <  2:639075/139‑1 (MQ=255)

            atatGACCGGCGATGCGGTTGGGCCAAATATGATTAATTTCTGGAAGAATGTCAGTATCGCTGGCGCGTTCTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATgcg                                                                                                                     >  1:241578/1‑139 (MQ=255)

               tGACCGGCGATGCGGTTGGGCCAAATATGATTAATTTCTGGAAGAATGTCAGTATCGCTGGCGCGTTCTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATgcggcg                                                                                                                  >  2:482620/1‑139 (MQ=255)

               tGACCGGCGATGCGGTTGGGCCAAATATGATTAATTTCTGGAAGAATGTCAGTATCGCTGGCGCGTTCTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATgcggcg                                                                                                                  >  1:637695/1‑139 (MQ=255)

               tGACCGGCGATGCGGTTGGGCCAAATATGATTAATTTCTGGAAGAATGTCAGTATCGCTGGCGCGTTCTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATgcggcg                                                                                                                  >  1:509793/1‑139 (MQ=255)

                 aCCGGCGATGCGGTTGGGCCAAATATGATTAATTTCTGGAAGAATGTCAGTATCGCTGGCGCGTTCTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATGCGGCGTg                                                                                                                <  2:1020419/139‑1 (MQ=255)

                  ccGGCGATGCGGTTGGGCCAAATATGATTAATTTCTGGAAGAATGTCAGTATCGCTGGCGCGTTCTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATGCGGCGTGa                                                                                                               <  2:132728/139‑1 (MQ=255)

                     gCGATGCGGTTGGGCCAAATATGATTAATTTCTGGAAGAATGTCAGTATCGCTGGCGCGTTCTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATGCGGCGTGAACg                                                                                                            >  2:954243/1‑139 (MQ=255)

                     gCGATGCGGTTGGGCCAAATATGATTAATTTCTGGAAGAATGTCAGTATCGCTGGCGCGTTCTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATGCGGCGTGAACg                                                                                                            >  2:133364/1‑139 (MQ=255)

                         tGCGGTTGGGCCAAATATGATTAATTTCTGGAAGAATGTCAGTATCGCTGGCGCGTTCTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCtt                                                                                                        >  2:422509/1‑139 (MQ=255)

                            ggTTGGGCCAAATATGATTAATTTCTGGAAGAATGTCAGTATCGCTGGCGCGTTCTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCTTATc                                                                                                     <  2:898708/139‑1 (MQ=255)

                                gggCCAAATATGATTAATTTCTGGAAGAATGTCAGTATCGCTGGCGCGTTCTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGc                                                                                                 <  2:995894/139‑1 (MQ=255)

                                       atatGATTAATTTCTGGAAGAATGTCAGTATCGCTGGCGCGTTCTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGCATTtaat                                                                                          <  2:241578/139‑1 (MQ=255)

                                       atatGATTAATTTCTGGAAGAATGTCAGTATCGCTGGCGCGTTCTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGCATTtaat                                                                                          <  1:475853/139‑1 (MQ=255)

                                               aaTTTCTGGAAGAATGTCAGTATCGCTGGCGCGTTCTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGCATTTAATAAATTACa                                                                                  <  2:236615/139‑1 (MQ=255)

                                                     tGGAAGAATGTCAGTATCGCTGGCGCGTTCTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATGCGGCGTGa                                                                                                               >  1:513434/1‑104 (MQ=255)

                                                     tGGAAGAATGTCAGTATCGCTGGCGCGTTCTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATGCGGCGTGa                                                                                                               <  2:513434/104‑1 (MQ=255)

                                                     tGGAAGAATGTCAGTATCGCTGGCGCGTTCTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGCATTTAATAAATTACAGCCAct                                                                            <  2:998920/139‑1 (MQ=255)

                                                             tGTCAGTATCGCTGGCGCGTTCTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGCATTTAATAAATTACAGCCACTCTACCCGc                                                                    >  1:537534/1‑139 (MQ=255)

                                                                  gTATCGCTGGCGCGTTCTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGCATTTAATAAATTACAGCCACTCTACCCGCAACGa                                                               <  1:133364/139‑1 (MQ=255)

                                                                  gTATCGCTGGCGCGTTCTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGCATTTAATAAATTACAGCCACTCTACCCGCAACGa                                                               <  1:149360/139‑1 (MQ=255)

                                                                  gTATCGCTGGCGCGTTCTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGCATTTAATAAATTACAGCCACTCTACCCGCAACGa                                                               <  1:298594/139‑1 (MQ=255)

                                                                  gTATCGCTGGCGCGTTCTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGCATTTAATAAATTACAGCCACTCTACCCGCAACGa                                                               <  1:422509/139‑1 (MQ=255)

                                                                  gTATCGCTGGCGCGTTCTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGCATTTAATAAATTACAGCCACTCTACCCGCAACGa                                                               <  2:337574/139‑1 (MQ=255)

                                                                   tagcccTGGCGCCTTCTTGCTATTGGGAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGCATTTAATAAATTACAGCCACTCTACCCGCAACGAc                                                              <  2:3705/134‑1 (MQ=39)

                                                                     tCGCTGGCGCGTTCTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGCATTTAATAAATTACAGCCACTCTACCCGCAACGACAt                                                            >  1:754347/1‑139 (MQ=255)

                                                                        cTGGCGCGTTCTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGCATTTAATAAATTACAGCCACTCTACCCGCAACGACAtctc                                                         >  1:1025432/1‑139 (MQ=255)

                                                                                  cTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGCATTTAATAAATTACAGCCa                                                                              <  1:946903/108‑1 (MQ=255)

                                                                                  cTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGCATTTAATAAATTACAGCCa                                                                              >  2:946903/1‑108 (MQ=255)

                                                                                    tGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGCATTTAATAAATTACAGCCACTCTACCCGCAACGACATCTCTGAAGTTGTTGa                                             <  2:537534/139‑1 (MQ=255)

                                                                                                   ccgggccgggGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGCATTTAATAAATTACAGCCACTCTACCCGCAACGACATCTCTGAAGTTGTTGATTCCCCTGGTGCTAg                              >  2:167412/1‑139 (MQ=255)

                                                                                                      ggccgggGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATGTGGCGTGAACGCCTTATCCGGCATTTAATAAATTACAGCCACTCTACCCGCAACGACATCTCTGAAGTTGTTGATTCCCCTGGTg                                  >  1:157817/1‑132 (MQ=255)

                                                                                                      ggccgggGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATGTGGCGTGAACGCCTTATCCGGCATTTAATAAATTACAGCCACTCTACCCGCAACGACATCTCTGAAGTTGTTGATTCCCCTGGTg                                  <  2:157817/132‑1 (MQ=255)

                                                                                                      ggccgggGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGCATTTAATAAATTACAGCCACTCTACCCGCAACGACATCTCTGAAGTTGTTGATTCCCCTGGTGCTAgcgc                           >  2:172060/1‑139 (MQ=255)

                                                                                                       gccgggGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGCATTtaat                                                                                          >  2:948157/1‑75 (MQ=255)

                                                                                                       gccgggGGCAATTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGCATTtaat                                                                                          <  1:948157/75‑1 (MQ=255)

                                                                                                                 aTTTCTCTCGATCGGCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGCATTTAATAAATTACAGCCACTCTACCCGCAACGACATCTCTGAAGTTGTTGATTCCCCTGGTGCTAGCGCAATGAGATCAc                <  1:482620/139‑1 (MQ=255)

                                                                                                                          gATCGGCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGCATTTAATAAATTACAGTCACTCTACCCGCAACGACATCTCTGAAGTTGTTGATTCCCCTGGTGCTAGCGCAATGAGATCACCCCCTTCCg       >  1:418567/1‑139 (MQ=255)

                                                                                                                            tCGGCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGCATTta                                                                                            <  1:864183/52‑1 (MQ=255)

                                                                                                                            tCGGCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGCATTta                                                                                            >  2:864183/1‑52 (MQ=255)

                                                                                                                            tCGGCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGCATTTAATAAATTACAGCCACTCTACCCGCAACGACATCTCTGAAGTTGTTGATTCCCCTGGTGCTAGCGCAATGAGATCACCCCCTTCCggg     <  1:167412/139‑1 (MQ=255)

                                                                                                                             cGGCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGCATTTAATAAATTACAGCCACTCTACCCGCAACGACATCTCTGAAGTTGTTGATTCCCCTGGTGCTAGCGCAATGAGATCACCCCCTTCCGGGc    >  1:987127/1‑139 (MQ=255)

                                                                                                                               gCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGCATTTAATAAATTACAGCCACTCTa                                                                         <  1:727938/68‑1 (MQ=255)

                                                                                                                               gCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGCATTTAATAAATTACAGCCACTCTa                                                                         >  2:727938/1‑68 (MQ=255)

                                                                                                                               gCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGCATTTAATAAATTACAGCCACTCTACCCGCAACGACATCTCTGAAGTTGTTGATTCCCCt                                      >  1:151699/1‑103 (MQ=255)

                                                                                                                               gCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGCATTTAATAAATTACAGCCACTCTACCCGCAACGACATCTCTGAAGTTGTTGATTCCCCt                                      <  2:151699/103‑1 (MQ=255)

                                                                                                                               gCGTTAAGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGCATTTAATAAATTACAGCCACTCTACCCGCAACGACATCTCTGAAGTTGTTGATTCCCCTGGTGCTAGCGCAATGAGATCACCCCCTTCCGGGCga  <  2:464781/139‑1 (MQ=255)

ACCATTACTGGGATATGACCGGCGATGCGGTTGGGCCAAATATGATTAATTTCTGGAAGAATGTCAGTATCGCTGGCGCGTTCTTGCTATTGGCAATTACCGGGCCGGGGGCAATTTCTCTCGATCGGCGTTAGGAAAGATGCCGGATGCGGCGTGAACGCCTTATCCGGCATTTAATAAATTACAGCCACTCTACCCGCAACGACATCTCTGAAGTTGTTGATTCCCCTGGTGCTAGCGCAATGAGATCACCCCCTTCCGGGCGA  >  NC_000913/2673635‑2673900

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `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