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
A2 F5 I184 R1	278	29.6	1166432	97.3%	1134938	124.1

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%	102.8 / NA	30	E178G (GAA→GGA)	folD	bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (12/18); total (12/18)

CTTTGATCCAGTCACCGGGAATAAAGCCTGGCTTGCCAACGGCAACGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTTCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACCGCGCGGGGTGCAGGGACGCAGA  >  NZ_CP009273/552531‑552787

cttTGATCCAGTCACCGGGAATAAAGCCTGGCTTGCCAACGGCAACGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCa                                                                                                                         <  1:92726/138‑1 (MQ=255)

         aGTCACCGGGAATAAAGCCTGGCTTGCCAACGGCAACGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCgg                                                                                                               >  2:156316/1‑139 (MQ=255)

           tCACCGGGAATAAAGCCTGGCTTGCCAACGGCAACGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGggc                                                                                                             >  1:139503/1‑139 (MQ=255)

                gggAATAAAGCCTGGCTTGCCAACGGCAACGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCa                                                                                                        <  1:51209/139‑1 (MQ=255)

                                         gCAACGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATcacca                                                                               >  2:119388/1‑139 (MQ=255)

                                           aaCGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACg                                                                             <  2:351415/139‑1 (MQ=255)

                                            aCGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACgg                                                                            >  1:467357/1‑139 (MQ=255)

                                                tCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGtt                                                                        <  2:139503/139‑1 (MQ=255)

                                                acAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGtt                                                                        <  1:196571/138‑1 (MQ=255)

                                                        tCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGa                                                                <  2:467357/139‑1 (MQ=255)

                                                         cGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCggg                                                                                                              <  1:311174/92‑1 (MQ=255)

                                                         cGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCggg                                                                                                              >  2:311174/1‑92 (MQ=255)

                                                         cGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCg                                                                 >  1:30390/1‑137 (MQ=255)

                                                          ggCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGaa                                                               <  1:156316/138‑1 (MQ=255)

                                                          ggCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAg                                                              >  2:430691/1‑139 (MQ=255)

                                                                                  aTTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAagc                                      <  2:227619/139‑1 (MQ=255)

                                                                                       tAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCg                                  <  1:78634/138‑1 (MQ=255)

                                                                                            aaGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTAt                                                          <  2:195524/109‑1 (MQ=255)

                                                                                            aaGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTAt                                                          >  1:195524/1‑109 (MQ=255)

                                                                                               cGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATAc                         >  2:95256/1‑139 (MQ=255)

                                                                                                     gTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACcgcgcg                   <  1:551594/139‑1 (MQ=255)

                                                                                                     gTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACcgcgcg                   <  2:30390/139‑1 (MQ=255)

                                                                                                     gTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACcgcgcg                   <  1:291759/139‑1 (MQ=255)

                                                                                                     gTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACcgcgcg                   <  1:257303/139‑1 (MQ=255)

                                                                                                     gTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACcgcgcg                   <  1:188626/139‑1 (MQ=255)

                                                                                                     gTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCAAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACcgcgcg                   <  1:388995/139‑1 (MQ=255)

                                                                                                                      aCCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACg                                             <  1:472326/96‑1 (MQ=255)

                                                                                                                      aCCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACg                                             >  2:472326/1‑96 (MQ=255)

                                                                                                                      aCCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACCGCGCGGGGTGCAGGGACGCAGa  >  1:516570/1‑139 (MQ=255)

                                                                                                                      aCCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACCGCGCGGGGTGCAGGGACGCAGa  >  1:130641/1‑139 (MQ=255)

CTTTGATCCAGTCACCGGGAATAAAGCCTGGCTTGCCAACGGCAACGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTTCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACCGCGCGGGGTGCAGGGACGCAGA  >  NZ_CP009273/552531‑552787

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

TCTTTGATCCAGTCACCGGGAATAAAGCCTGGCTTGCCAACGGCAACGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTTCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACCGCGCGGGGTGCAGGGACGCAGACGCGGCGCGCGCTGG  >  NZ_CP009273/552530‑552802

TCTTTGATCCAGTCACCGGGAATAAAGCCTGGCTTGCCAACGGCAACGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGG                                                                                                                             <  SRR3722139.93833/150‑1 (MQ=60)

 CTTTGATCCAGTCACCGGGAATAAAGCCTGGCTTGCCAACGGCAACGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCG                                                                                                                           >  SRR3722139.141186/1‑151 (MQ=60)

          acggtctcgtgggctcggagatgtgtataagagacagGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGAT                                                                                                                  <  SRR3722139.315029/114‑1 (MQ=60)

                CGGGAATAAAGCCTGGCTTGCCAACGGCAACGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGA                                                                                                            <  SRR3722139.51795/151‑1 (MQ=60)

                                  TGCCAACGGCAACGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGC                                                                                          >  SRR3722139.472816/1‑151 (MQ=60)

                                               GATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGA                                                                               >  SRR3722139.30735/1‑149 (MQ=60)

                                                gaCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGG                                                                            <  SRR3722139.198997/149‑1 (MQ=60)

                                                          CGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGT                                                                   <  SRR3722139.158227/150‑1 (MQ=60)

                                                                              cgtgggctcggagatgtgtataagagacagGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCG                                                 <  SRR3722139.477829/118‑1 (MQ=60)

                                                                                  GATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACtgtctcttatacacatctc                                          >  SRR3722139.197933/1‑132 (MQ=60)

                                                                                       TTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACCG                                      <  SRR3722139.79541/150‑1 (MQ=60)

                                                                                                     AGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACCGCGCGGGGTGCAGGGA                       <  SRR3722139.190968/151‑1 (MQ=60)

                                                                                                     AGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACCGCGCGGGGTGCAGGGA                       <  SRR3722139.557934/151‑1 (MQ=60)

                                                                                                     AGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACCGCGCGGGGTGCAGGGA                       <  SRR3722139.295428/151‑1 (MQ=60)

                                                                                                     AGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACCGCGCGGGGTGCAGGGA                       <  SRR3722139.260541/151‑1 (MQ=60)

                                                                                                     AGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCAAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACCGCGCGGGGTGCAGGGA                       <  SRR3722139.393616/151‑1 (MQ=60)

                                                                                                            GTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACCGCGCGGGGTGCAGGGACGCAGAC                >  SRR3722139.522504/1‑151 (MQ=60)

                                                                                                            GTAGTGGTGCAACCTGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACCGCGCGGGGTGCAGGGACGCAGAC                >  SRR3722139.132245/1‑151 (MQ=60)

                                                                                                                          TGCCAGCAGCAGTCCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACtgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgccgtcttc  >  SRR3722139.209960/1‑92 (MQ=60)

TCTTTGATCCAGTCACCGGGAATAAAGCCTGGCTTGCCAACGGCAACGATCAATAGATCGGCATTTTCTACGTGATGACGCAGATTTTTAGTGAAGCGGTGAGTCACTGTAGTGGTGCAACCTGCCAGCAGCAGTTCCATGCTCATCGGGCGGCCAACGATATTCGATGCGCCAATCACCACGGCGTTGAGGCCGAAGGTATCAATGTTGTAACGCTCAAGCAGCGTGACGATACCGCGCGGGGTGCAGGGACGCAGACGCGGCGCGCGCTGG  >  NZ_CP009273/552530‑552802

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`