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 F4 I96 R1	227	23.3	882352	98.0%	864704	126.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	552,665	T→C	E178G (GAA→GGA)	folD ←	bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	552,665	0	T	C	100.0%	106.3 / NA	29	E178G (GAA→GGA)	folD	bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (16/13); total (16/13)

CAGTCACCGGGAATAAAGCCTGGCTTGCCAACGGCAACGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTTCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACCGCGCGGGGTGCAGGGACGCAGACGCGGCGCGCG  >  NZ_CP009273/552539‑552798

cAGTCACCGGGAATAAAGCCTGGCTTGCCAACGGCAACGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATc                                                                                                                            <  1:33678/138‑1 (MQ=255)

   tCACCGGGAATAAAGCCTGGCTTGCCAACGGCAACGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGggc                                                                                                                        >  2:361409/1‑139 (MQ=255)

                    tGGCTTGCCAACGGCAACGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGAt                                                                                                       >  2:57391/1‑139 (MQ=255)

                      gCTTGCCAACGGCAACGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATgc                                                                                                     >  2:429708/1‑139 (MQ=255)

                       cTTGCCAACGGCAACGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATgcg                                                                                                    <  1:361409/139‑1 (MQ=255)

                           ccAACGGCAACGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCa                                                                                                 <  2:123521/138‑1 (MQ=255)

                                ggCAACGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATcac                                                                                            >  2:340345/1‑138 (MQ=255)

                                            tAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAgg                                                                               >  1:383939/1‑139 (MQ=255)

                                               aTCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGcc                                                                             >  1:289713/1‑138 (MQ=255)

                                                tCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGa                                                                           <  1:351593/139‑1 (MQ=255)

                                                 cGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCg                                                                            >  1:22134/1‑137 (MQ=255)

                                                 cGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCg                                                                            >  1:378826/1‑137 (MQ=255)

                                                      ttttCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTAt                                                                     <  1:87372/139‑1 (MQ=255)

                                                             cGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAAtgtt                                                              >  2:303977/1‑139 (MQ=255)

                                                               tgatgaCGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAAtgttgt                                                            <  2:53783/139‑1 (MQ=255)

                                                                 atgaCGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTaa                                                          <  2:107583/139‑1 (MQ=255)

                                                                 atgaCGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTaa                                                          >  1:371725/1‑139 (MQ=255)

                                                                                             gTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACcgcgcg                              <  1:392960/139‑1 (MQ=255)

                                                                                             gTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACcgcgcg                              <  2:29350/139‑1 (MQ=255)

                                                                                             gTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACcgcgcg                              <  2:378826/139‑1 (MQ=255)

                                                                                                 cTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACcgcgcg                              <  2:88806/135‑1 (MQ=255)

                                                                                                 cTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACcgcgcg                              >  1:88806/1‑135 (MQ=255)

                                                                                                      gtggtgCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGcc                                                                             <  2:360297/83‑1 (MQ=255)

                                                                                                      gtggtgCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGcc                                                                             >  1:360297/1‑83 (MQ=255)

                                                                                                      gtggtgCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACCGCGCGGGGTGCAgg                     >  2:183390/1‑139 (MQ=255)

                                                                                                            cAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACCGCGCGGGGTGCAGGGACg                 >  2:301277/1‑137 (MQ=255)

                                                                                                                 tGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACCGCGCGGGGTGCAGGGACGCAGAcgc          >  2:382235/1‑139 (MQ=255)

                                                                                                                    cagcagcagTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACCGCGCGGGGTGCAGGGACGCAGACgcggc       >  1:248478/1‑139 (MQ=255)

                                                                                                                         gcagTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACCGCGCGGGGTGCAGGGACGCAGACGCGgcgcgcg  <  2:383939/139‑1 (MQ=255)

CAGTCACCGGGAATAAAGCCTGGCTTGCCAACGGCAACGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTTCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACCGCGCGGGGTGCAGGGACGCAGACGCGGCGCGCG  >  NZ_CP009273/552539‑552798

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

CACAATTGCGCCTTCTTTGATCCAGTCACCGGGAATAAAGCCTGGCTTGCCAACGGCAACGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTTCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACCGCGCGGGGTGCAGGGACGCAGACGCGGCGCGCGCTGGCACAGACGACC  >  NZ_CP009273/552517‑552813

CACAATTGCGCCTTCTTTGATCCAGTCACCGGGAATAAAGCCTGGCTTGCCAACGGCAACGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCC                                                                                                                                                     <  SRR3722119.376456/150‑1 (MQ=60)

                     CCAGTCACCGGGAATAAAGCCTGGCTTGCCAACGGCAACGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAAC                                                                                                                                <  SRR3722119.33964/150‑1 (MQ=60)

                                            GCTTGCCAACGGCAACGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCAC                                                                                                        <  SRR3722119.365057/151‑1 (MQ=60)

                                                       GCAACGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGC                                                                                             >  SRR3722119.387808/1‑151 (MQ=60)

                                                          ACGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCG                                                                                           >  SRR3722119.292685/1‑150 (MQ=60)

                                                            GATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGA                                                                                          >  SRR3722119.22336/1‑149 (MQ=60)

                                                            GATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGA                                                                                          >  SRR3722119.382639/1‑149 (MQ=60)

                                                                     ATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATG                                                                               <  SRR3722119.355165/151‑1 (MQ=60)

                                                                           ATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAA                                                                         <  SRR3722119.88229/151‑1 (MQ=60)

                                                                            TTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAAC                                                                        >  SRR3722119.375476/1‑151 (MQ=60)

                                                                                                            GCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACCGCGCGGGGTG                                        >  SRR3722119.89681/1‑151 (MQ=60)

                                                                                                                 GAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAActgtctcttatacacatctccgagcccacgagactaaggcgaatct                                   >  SRR3722119.363937/1‑105 (MQ=60)

                                                                                                                  AGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACCGCGCGGGGTGCAGGGA                                  <  SRR3722119.396885/151‑1 (MQ=60)

                                                                                                                               GTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACCGCGCGGGGTGCAGGGACGCAGACGCGGCG                     >  SRR3722119.251058/1‑151 (MQ=60)

                                                                                                                                           AGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACCGCGCGGGGTGCAGGGACGCAGACGCGGCGCGCGCTGGCAC          >  SRR3722119.260644/1‑150 (MQ=60)

                                                                                                                                                  GTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGCGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACCGCGCGGGGTGCAGGGACGCAGACGCGGCGCGCGCTGGCACAGACGACC  >  SRR3722119.169027/1‑151 (MQ=60)

CACAATTGCGCCTTCTTTGATCCAGTCACCGGGAATAAAGCCTGGCTTGCCAACGGCAACGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTTCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACCGCGCGGGGTGCAGGGACGCAGACGCGGCGCGCGCTGGCACAGACGACC  >  NZ_CP009273/552517‑552813

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 17 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`