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 F2 I225 R1	227	21.4	1179702	97.1%	1145490	86.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,852,078	T→G	T467P (ACG→CCG)	yidK ←	solute:sodium symporter family transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,852,078	0	T	G	100.0%	108.7 / NA	33	T467P (ACG→CCG)	yidK	solute:sodium symporter family transporter
Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (13/20); total (13/20)

CCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGTACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCCCCATCGC  >  NZ_CP009273/3851991‑3852162

ccGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAACCCGATCACCAGCATCACGACCACGTTGATGCAGAACGGAc                                                                                    <  1:480525/90‑1 (MQ=255)

ccGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGAc                                                                                    <  1:521016/90‑1 (MQ=255)

ccGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGAc                                                                                    <  1:18435/90‑1 (MQ=255)

ccGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGAc                                                                                    >  1:185566/1‑90 (MQ=255)

ccGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGAc                                                                                    <  1:259481/90‑1 (MQ=255)

ccGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGAc                                                                                    >  1:289804/1‑90 (MQ=255)

  gCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAg                                                                                  <  2:444980/90‑1 (MQ=255)

     aaCGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGcc                                                                               <  2:289804/90‑1 (MQ=255)

          aTCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGcac                                                                          >  1:136937/1‑90 (MQ=255)

                   ggTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGaa                                                                 >  2:155454/1‑90 (MQ=255)

                            cGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTc                                                        <  2:185566/90‑1 (MQ=255)

                              tGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGa                                                      >  2:133624/1‑90 (MQ=255)

                                gcgcgcGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAAc                                                    <  2:430482/90‑1 (MQ=255)

                                   cgcgGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTc                                                 <  1:211788/90‑1 (MQ=255)

                                    gcgGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCa                                                >  2:461009/1‑90 (MQ=255)

                                          tGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGAt                                          <  2:369970/90‑1 (MQ=255)

                                          tGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGAt                                          <  1:136366/90‑1 (MQ=255)

                                          tGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGAt                                          <  2:135669/90‑1 (MQ=255)

                                               aaaCCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTg                                     >  1:131045/1‑90 (MQ=255)

                                                   cGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATgg                                 <  1:155454/90‑1 (MQ=255)

                                                    gATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGt                                <  1:544785/90‑1 (MQ=255)

                                                           aGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAg                         >  1:351595/1‑90 (MQ=255)

                                                            gCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGc                        <  2:131045/90‑1 (MQ=255)

                                                            gCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGc                        <  1:494986/90‑1 (MQ=255)

                                                            gCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGc                        <  1:39070/90‑1 (MQ=255)

                                                                 aCGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGAtt                   <  2:403053/90‑1 (MQ=255)

                                                                       aCGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGtt                                      >  2:237419/1‑65 (MQ=255)

                                                                       aCGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGtt                                      <  1:237419/65‑1 (MQ=255)

                                                                           tGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATcc         <  2:149633/90‑1 (MQ=255)

                                                                           tGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATcc         >  1:203838/1‑90 (MQ=255)

                                                                            gATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATccc        >  1:13436/1‑90 (MQ=255)

                                                                            gATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATccc        >  2:403702/1‑90 (MQ=255)

                                                                                  gAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCCCCATCGc  >  2:538065/1‑90 (MQ=255)

CCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGTACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCCCCATCGC  >  NZ_CP009273/3851991‑3852162

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

GTTTCATGTCCACCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGTACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCCCCATCGCTACTTTT  >  NZ_CP009273/3851979‑3852169

GTTTCATGTCCACCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGG                                                                                             >  SRR3722109.555372/1‑100 (MQ=60)

  TTCATGTCCACCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGAC                                                                                           >  SRR3722109.293508/1‑100 (MQ=60)

  TTCATGTCCACCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGAC                                                                                           >  SRR3722109.187850/1‑100 (MQ=60)

            gagatctacacattgacattcgtcggcagcgtcagatgtgtataagagacagGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCAC                                                                                 <  SRR3722109.467334/48‑1 (MQ=60)

            CCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAACCCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCAC                                                                                 <  SRR3722109.487762/100‑1 (MQ=60)

            CCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCAC                                                                                 <  SRR3722109.262626/100‑1 (MQ=60)

            CCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCAC                                                                                 <  SRR3722109.528951/100‑1 (MQ=60)

            CCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCAC                                                                                 <  SRR3722109.18672/100‑1 (MQ=60)

            CCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCAC                                                                                 >  SRR3722109.138627/1‑100 (MQ=60)

                                               CGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGT                                              <  SRR3722109.214336/100‑1 (MQ=60)

                                                 CGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTG                                            >  SRR3722109.132649/1‑100 (MQ=60)

                                                      TGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGT                                       <  SRR3722109.138054/100‑1 (MQ=60)

                                                          gtgtataagagaCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATG                                   <  SRR3722109.240220/88‑1 (MQ=60)

                                                             ACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAG                                >  SRR3722109.356374/1‑100 (MQ=60)

                                                               CGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCT                              <  SRR3722109.157374/100‑1 (MQ=60)

                                                                GATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTG                             <  SRR3722109.553047/100‑1 (MQ=60)

                                                                        GCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCC                     <  SRR3722109.39528/100‑1 (MQ=60)

                                                                        GCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCC                     <  SRR3722109.502460/100‑1 (MQ=60)

                                                                             ACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCC                >  SRR3722109.206312/1‑100 (MQ=60)

                                                                              CGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCCC               >  SRR3722109.13620/1‑100 (MQ=60)

                                                                                           GCAGAACGGACAGGCCAGCACATAGAGGCAATGGAAGTCGAACTTCACCAGAGAGTTGATGGAGATGTAGCTGATTATTCCAATCCCCCTCTCTACTTTT  >  SRR3722109.341963/1‑100 (MQ=60)

GTTTCATGTCCACCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGTACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCCCCATCGCTACTTTT  >  NZ_CP009273/3851979‑3852169

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 25 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`