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 F5 I97 R1	275	44.0	1733530	96.5%	1672856	122.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	771,797	A→G	intergenic (+64/‑1)	tolR → / → tolA	colicin uptake protein TolR/cell envelope integrity protein TolA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	771,797	0	A	G	100.0%	100.4 / NA	30	intergenic (+64/‑1)	tolR/tolA	colicin uptake protein TolR/cell envelope integrity protein TolA
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (21/9); total (21/9)

ATTAAAGCACTGAACTTGTTACATAGTGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGAGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGCTGATCTGGAGTTCGTTCGATGAGAATATAGAAGCTTCAGCCGGAGG  >  NZ_CP009273/771665‑771928

atTAAAGCACTGAACTTGTTACATAGTGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTc                                                                                                                                >  1:3687/1‑138 (MQ=255)

   aaaGCACTGAACTTGTTACATAGTGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAg                                                                                                                            >  2:385807/1‑139 (MQ=255)

     aGCACTGAACTTGTTACATAGTGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAgg                                                                                                                           >  1:80612/1‑138 (MQ=255)

     aGCACTGAACTTGTTACATAGTGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAgg                                                                                                                           >  1:147915/1‑138 (MQ=255)

          tGAACTTGTTACATAGTGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAAcc                                                                                                                      >  2:755506/1‑138 (MQ=255)

          tGAACTTGTTACATAGTGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAAcc                                                                                                                      >  2:136588/1‑138 (MQ=255)

                          tGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCt                                                                                                     >  1:33104/1‑139 (MQ=255)

                           gCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCt                                                                                                     >  1:516775/1‑138 (MQ=255)

                            cGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTc                                                                                                    >  2:679624/1‑138 (MQ=255)

                              ggTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAg                                                                                                 <  1:27877/139‑1 (MQ=255)

                                    aaaTCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGc                                                                                            >  1:584318/1‑138 (MQ=255)

                                                  aaTGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTcag                                                                              <  1:661440/138‑1 (MQ=255)

                                                        gCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCAGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGtgat                                                                       <  1:597991/139‑3 (MQ=255)

                                                         cAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGtgctg                                                                      >  1:566217/1‑139 (MQ=255)

                                                         cAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGtgctg                                                                      >  2:590250/1‑139 (MQ=255)

                                                                      cATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAattat                                                                                   >  2:708364/1‑113 (MQ=255)

                                                                      cATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAattat                                                                                   <  1:708364/113‑1 (MQ=255)

                                                                          tGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTgc                                                     >  1:28219/1‑139 (MQ=255)

                                                                          tGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTgc                                                     >  2:797058/1‑139 (MQ=255)

                                                                              tttCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTgcggcg                                                 <  2:584318/139‑1 (MQ=255)

                                                                                 cccTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGCt                                               >  2:299338/1‑138 (MQ=255)

                                                                                 cccTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGCt                                               >  1:388319/1‑138 (MQ=255)

                                                                                                gagCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAg                                                                                                 <  2:55173/73‑1 (MQ=255)

                                                                                                gagCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAg                                                                                                 >  1:55173/1‑73 (MQ=255)

                                                                                                 agCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGCTGATCTGGAgttcgttc                               >  1:624586/1‑138 (MQ=255)

                                                                                                 agCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGACAAAGGCGACCGAACAAAACGTCAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGGCATCTTAGTTGCGGCGATGATCTGGAgttcgttc                               >  2:548836/1‑138 (MQ=255)

                                                                                                  gCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGCTGATCTGGAGTTCGTTCGa                             >  2:467731/1‑139 (MQ=255)

                                                                                                   cGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGCTGATCTGGAGTTCGTTCGAt                            <  2:388319/139‑1 (MQ=255)

                                                                                                      gTAACAGGCGAACAGTTTTGGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTTATCTTATTTGCGGCGCTGATCTGGAGTTCGTTCGATgag                         <  1:548836/139‑1 (MQ=255)

                                                                                                                             aaCCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGCTGATCTGGAGTTCGTTCGATGAGAATATAGAAGCTTCAGCCGGAgg  <  1:590250/139‑1 (MQ=255)

ATTAAAGCACTGAACTTGTTACATAGTGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGAGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGCTGATCTGGAGTTCGTTCGATGAGAATATAGAAGCTTCAGCCGGAGG  >  NZ_CP009273/771665‑771928

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `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

TACGATGAAATAATTAAAGCACTGAACTTGTTACATAGTGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGAGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGCTGATCTGGAGTTCGTTCGATGAGAATATAGAAGCTTCAGCCGGAGGCGGCGGTGGTTCGTCC  >  NZ_CP009273/771653‑771944

TACGATGAAATAATTAAAGCACTGAACTTGTTACATAGTGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTC                                                                                                                                                <  SRR3722120.140775/150‑1 (MQ=60)

 ACGATGAAATAATTAAAGCACTGAACTTGTTACATAGTGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCA                                                                                                                                               >  SRR3722120.3731/1‑150 (MQ=60)

      GAAATAATTAAAGCACTGAACTTGTTACATAGTGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGC                                                                                                                                          >  SRR3722120.149909/1‑150 (MQ=60)

      GAAATAATTAAAGCACTGAACTTGTTACATAGTGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGC                                                                                                                                          >  SRR3722120.81661/1‑150 (MQ=60)

      GAAATAATTAAAGCACTGAACTTGTTACATAGTGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGC                                                                                                                                          <  SRR3722120.335856/150‑1 (MQ=60)

                           TTGTTACATAGTGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTC                                                                                                                    >  SRR3722120.33502/1‑151 (MQ=60)

                            TGTTACATAGTGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTC                                                                                                                    >  SRR3722120.524136/1‑150 (MQ=60)

                             GTTACATAGTGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCtgtctcttatacacatctccgagc                                                                                                                  >  SRR3722120.685243/1‑127 (MQ=60)

                                     GTGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCG                                                                                                           >  SRR3722120.592454/1‑150 (MQ=60)

                                         GGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAAT                                                                                                      <  SRR3722120.28191/151‑1 (MQ=60)

                                                        gtgtataagagacagGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGC                                                                                        <  SRR3722120.718033/135‑1 (MQ=60)

                                                          GTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGC                                                                                     >  SRR3722120.574131/1‑151 (MQ=60)

                                                             TAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCAT                                                                                   <  SRR3722120.670514/150‑1 (MQ=60)

                                                                   CGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCAGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGATGCATGTCATCT                                                                            <  SRR3722120.606307/151‑1 (MQ=60)

                                                                           ATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCG                                                                    >  SRR3722120.28537/1‑151 (MQ=60)

                                                                                  CATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGCTG                                                              >  SRR3722120.394018/1‑150 (MQ=60)

                                                                                                 TGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATctgtctcttatacacatctccgagcccacgagactaaggcgaatctcgtatgccgt                                              >  SRR3722120.55852/1‑95 (MQ=60)

                                                                                                  GCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGCTGATCTGGAGTTCGTTCG                                              >  SRR3722120.633256/1‑150 (MQ=60)

                                                                                                                 GGTAACAGGCGAACAGTTTTGGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTTATCTTATTTGCGGCGCTGATCTGGAGTTCGTTCGATGAGAATATAGAAGC                              <  SRR3722120.556573/151‑1 (MQ=60)

                                                                                                                                        AAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGCTGATCTGGAGTTCGTTCGATGAGAATATAGAAGCTTCAGCCGGAGGCGGCGGTGGTT       <  SRR3722120.598486/151‑1 (MQ=60)

                                                                                                                                             GAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGCTGATCTGGAGTTCGTTCGATGAGAATATAGAAGCTTCAGCCGGAGGCGGCGGTGGTTCGTCC  <  SRR3722120.687153/151‑1 (MQ=60)

TACGATGAAATAATTAAAGCACTGAACTTGTTACATAGTGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGAGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGCTGATCTGGAGTTCGTTCGATGAGAATATAGAAGCTTCAGCCGGAGGCGGCGGTGGTTCGTCC  >  NZ_CP009273/771653‑771944

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 17 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`