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	771,555	A→G	E84G (GAG→GGG)	tolR →	colicin uptake protein TolR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	771,555	0	A	G	100.0%	96.1 / NA	29	E84G (GAG→GGG)	tolR	colicin uptake protein TolR
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (18/11); total (18/11)

CCCAGAGCGTGGAGGTCGATCTGCCAGACGCTACTGAATCACAGGCGGTGAGCAGTAACGATAATCCGCCAGTGATTGTTGAAGTGTCTGGTATTGGTCAGTACACCGTGGTGGTTGAGAAAGATCGCCTGGAGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTGGCGCAAAAGATGTGCCTTACGATGAAATAATTAAAGCACTGAACTTGTTACA  >  NZ_CP009273/771423‑771687

cccAGAGCGTGGAGGTCGATCTGCCAGACGCTACTGAATCACAGGCGGTGAGCAGTAACGATAATCCGCCAGTGATTGTTGAAGTGTCTGGTATTGGTCAGTACACCGTGGTGGTTGAGAAAGATCGCCTGGGGCGttt                                                                                                                                <  2:485633/139‑1 (MQ=255)

  cAGAGCGTGGAGGTCGATCTGCCAGACGCTACTGAATCACAGGCGGTGAGCAGTAACGATAATCCGCCAGTGATTGTTGAAGTGTCTGGTATTGGTCAGTACACCGTGGTGGTTGAGAAAGATCGCCTGGGGCGTTTac                                                                                                                              <  2:150624/139‑1 (MQ=255)

     agCGTGGAGGTCGATCTGCCAGACGCTACTGAATCACAGGCGGTGAGCAGTAACGATAATCCGCCAGTGATTGTTGAAGTGTCTGGTATTGGTCAGTACACCGTGGTGGTTGAGAAAGATCGCCTGGGGCGTTTaccac                                                                                                                           >  1:263346/1‑139 (MQ=255)

       cGTGGAGGTCGATCTGCCAGACGCTACTGAATCACAGGCGGTGAGCAGTAACGATAATCCGCCAGTGATTGTTGAAGTGTCTGGTATTGGTCAGTACACCGTGGTGGTTGAGAAAGATCGCCTGGGGCGTTTaccac                                                                                                                           >  1:573467/1‑137 (MQ=255)

                                    aaTCACAGGCGGTGAGCAGTAACGATAATCCGCCAGTGATTGTTGAAGTGTCTGGTATTGGTCAGTACACCGTGGTGGTTGAGAAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGc                                                                                              <  2:429273/137‑1 (MQ=255)

                                         caGGCGGTGCGCAGTAACGATAATCCGCCCGCGATTGTTGAAGTGTCTGGTATTGGTCAGGACACCGTGGTGGTTGAGCAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTc                                                                                        >  1:186519/1‑138 (MQ=255)

                                         caGGCGGTGAGCAGTAACGATAATCCGCCAGTGATTGTTGAAGTGTCTGGTATTGGTCAGTACACCGTGGTGGTTGAGAAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTc                                                                                        >  1:50069/1‑138 (MQ=255)

                                           ggCGGTGAGCAGTAACGATAATCCGCCAGTGATTGTTGAAGTGTCTGGTATTGGTCAGTACACCGTGGTGGTTGAGAAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAg                                                                                     >  1:319415/1‑139 (MQ=255)

                                                            aTAATCCGCCAGTGATTGTTGAAGTGTCTGGTATTGGTCAGTACACCGTGGTGGTTGAGAAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGt                                                                    >  1:159629/1‑139 (MQ=255)

                                                             tAATCCGCCAGTGATTGTTGAAGTGTCTGGTATTGGTCAGTACACCGTGGTGGTTGAGAAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTc                                                                   <  2:63960/139‑1 (MQ=255)

                                                                           ttgttgAAGTGTCTGGTATTGGTCAGTACACCGTGGTGGTTGAGAAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTgg                                                     <  2:502535/139‑1 (MQ=255)

                                                                              ttgAAGTGTCTGGTATTGGTCAGTACACCGTGGTGGTTGAGAAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTGgcgc                                                  <  1:224706/139‑1 (MQ=255)

                                                                                gaggtgtCTGGTATTGGTCAGTACACCGTGGTGGTTGAGAAAGAGCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTGGCGCa                                                 <  2:186519/135‑1 (MQ=255)

                                                                                      tCTGGTATTGGTCAGTACACCGTGGTGGTTGAGAAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTGGCGCAAAAGAt                                           <  2:438070/138‑1 (MQ=255)

                                                                                      tCTGGTATTGGTCAGTACACCGTGGTGGTTGAGAAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTGGCGCAAAAGAt                                           <  2:249050/138‑1 (MQ=255)

                                                                                                gTCAGTACACCGTGGTGGTTGAGAAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTGGCGCAAAAGATGTGCCTTACGa                                >  1:47554/1‑139 (MQ=255)

                                                                                                     tACACCGTGGTGGTTGAGAAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTGGCGCAAAAGATGTGCCTTACGATGaaa                           >  1:10727/1‑139 (MQ=255)

                                                                                                     tACACCGTGGTGGTTGAGAAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTGGCGCAAAAGATGTGCCTTACGATGaaa                           >  2:240079/1‑139 (MQ=255)

                                                                                                     tACACCGTGGTGGTTGAGAAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTGGCGCAAAAGATGTGCCTTACGATGaaa                           >  1:556735/1‑139 (MQ=255)

                                                                                                     tACACCGTGGTGGTTGAGAAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTGGCGCAAAAGATGTGCCTTACGATGaaa                           >  1:492285/1‑139 (MQ=255)

                                                                                                          cGTGGTGGTTGAGAAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTGGCGCAAAAGATGTGCCTTACGATGAaataat                       >  1:553637/1‑138 (MQ=255)

                                                                                                           gtggtgGTTGAGAAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTGGCGCAAAAGATGTGCCTTACGATGAAATAAtt                      >  2:468424/1‑138 (MQ=255)

                                                                                                               tggtTGAGAAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTGGCGCAAAAGATGTGCCTTACGATGAAATAATTAAAg                  >  2:204068/1‑138 (MQ=255)

                                                                                                               tggtTGAGAAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTGGCGCAAAAGATGTGCCTTACGATGAAATAATTAAAg                  >  2:149410/1‑138 (MQ=255)

                                                                                                               tggtTGAGAAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTGGCGCAAAAGATGTGCCTTACGATGAAATAATTAAAg                  >  1:419542/1‑138 (MQ=255)

                                                                                                                    gagaAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTGGCGCAAAAGATGTGCCTTACGATGAAATAATTAAAGCACTg             >  1:195813/1‑138 (MQ=255)

                                                                                                                           aTCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTGGCGCAAAAGATGTGCCTTACGATGAAATAATTAAAGCACTGAACTTGt      >  1:286325/1‑138 (MQ=255)

                                                                                                                              gCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTGGCGCAAAAGATGTGCCTTACGATGAAATAATTAAAGCACTGAACTTGTTACa  <  2:159629/139‑1 (MQ=255)

                                                                                                                              gCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTGGCGCAAAAGATGTGCCTTACGATGAAATAATTAAAGCACTGAACTTGTTACa  <  1:468424/139‑1 (MQ=255)

CCCAGAGCGTGGAGGTCGATCTGCCAGACGCTACTGAATCACAGGCGGTGAGCAGTAACGATAATCCGCCAGTGATTGTTGAAGTGTCTGGTATTGGTCAGTACACCGTGGTGGTTGAGAAAGATCGCCTGGAGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTGGCGCAAAAGATGTGCCTTACGATGAAATAATTAAAGCACTGAACTTGTTACA  >  NZ_CP009273/771423‑771687

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `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

GACAGCGCCCATCATCACCCAGAGCGTGGAGGTCGATCTGCCAGACGCTACTGAATCACAGGCGGTGAGCAGTAACGATAATCCGCCAGTGATTGTTGAAGTGTCTGGTATTGGTCAGTACACCGTGGTGGTTGAGAAAGATCGCCTGGAGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTGGCGCAAAAGATGTGCCTTACGATGAAATAATTAAAGCACTGAACTTGTTACATAGTGCGGGTGTGAAAT  >  NZ_CP009273/771406‑771704

GACAGCGCCCATCATCACCCAGAGCGTGGAGGTCGATCTGCCAGACGCTACTGAATCACAGGCGGTGAGCAGTAACGATAATCCGCCAGTGATTGTTGAAGTGTCTGGTATTGGTCAGTACACCGTGGTGGTTGAGAAAGATCGCCTGGGG                                                                                                                                                      <  SRR3722139.478136/151‑1 (MQ=60)

        CCATCATCACCCAGAGCGTGGAGGTCGATCTGCCAGACGCTACTGAATCACAGGCGGTGAGCAGTAACGATAATCCGCCAGTGATTGTTGAAGTGTCTGGTATTGGTCAGTACACCGTGGTGGTTGAGAAAGATCGCCTGGGGCGTTTACC                                                                                                                                              <  SRR3722139.565787/151‑1 (MQ=60)

           TCATCACCCAGAGCGTGGAGGTCGATCTGCCAGACGCTACTGAATCACAGGCGGTGAGCAGTAACGATAATCCGCCAGTGATTGTTGAAGTGTCTGGTATTGGTCAGTACACCGTGGTGGTTGAGAAAGATCGCCTGGGGCGTTTACCACC                                                                                                                                           >  SRR3722139.266651/1‑151 (MQ=60)

             ATCACCCAGAGCGTGGAGGTCGATCTGCCAGACGCTACTGAATCACAGGCGGTGAGCAGTAACGATAATCCGCCAGTGATTGTTGAAGTGTCTGGTATTGGTCAGTACACCGTGGTGGTTGAGAAAGATCGCCTGGGGCGTTTACCACC                                                                                                                                           >  SRR3722139.580025/1‑149 (MQ=60)

                                               CTACTGAATCACAGGCGGTGCGCAGTAACGATAATCCGCCCGCGATTGTTGAAGTGTCTGGTATTGGTCAGGACACCGTGGTGGTTGAGCAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCA                                                                                                        >  SRR3722139.188843/1‑150 (MQ=60)

                                               CTACTGAATCACAGGCGGTGAGCAGTAACGATAATCCGCCAGTGATTGTTGAAGTGTCTGGTATTGGTCAGTACACCGTGGTGGTTGAGAAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCA                                                                                                        >  SRR3722139.50646/1‑150 (MQ=60)

                                                 ACTGAATCACAGGCGGTGAGCAGTAACGATAATCCGCCAGTGATTGTTGAAGTGTCTGGTATTGGTCAGTACACCGTGGTGGTTGAGAAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGG                                                                                                     >  SRR3722139.323361/1‑151 (MQ=60)

                                                                  GAGCAGTAACGATAATCCGCCAGTGATTGTTGAAGTGTCTGGTATTGGTCAGTACACCGTGGTGGTTGAGAAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTC                                                                                    >  SRR3722139.161583/1‑151 (MQ=60)

                                                                                              GTTGAAGTGTCTGGTATTGGTCAGTACACCGTGGTGGTTGAGAAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTGGCGCAAAAGATGTGC                                                        <  SRR3722139.227457/151‑1 (MQ=60)

                                                                                                      GTCTGGTATTGGTCAGTACACCGTGGTGGTTGAGAAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTGGCGCAAAAGATGTGCCTTACGAT                                                >  SRR3722139.48106/1‑151 (MQ=60)

                                                                                                           GTATTGGTCAGTACACCGTGGTGGTTGAGAAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTGGCGCAAAAGATGTGCCTTACGATGAAAT                                           >  SRR3722139.10832/1‑151 (MQ=60)

                                                                                                           GTATTGGTCAGTACACCGTGGTGGTTGAGAAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTGGCGCAAAAGATGTGCCTTACGATGAAAT                                           >  SRR3722139.563115/1‑151 (MQ=60)

                                                                                                           GTATTGGTCAGTACACCGTGGTGGTTGAGAAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTGGCGCAAAAGATGTGCCTTACGATGAAAT                                           >  SRR3722139.497985/1‑151 (MQ=60)

                                                                                                                GGTCAGTACACCGTGGTGGTTGAGAAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTGGCGCAAAAGATGTGCCTTACGATGAAATAATT                                       >  SRR3722139.559994/1‑150 (MQ=60)

                                                                                                                     GTACACCGTGGTGGTTGAGAAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTGGCGCAAAAGATGTGCCTTACGATGAAATAATTAAAGC                                  >  SRR3722139.424503/1‑150 (MQ=60)

                                                                                                                          CCGTGGTGGTTGAGAAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTGGCGCAAAAGATGTGCCTTACGATGAAATAATTAAAGCACTGA                             >  SRR3722139.198229/1‑150 (MQ=60)

                                                                                                                                 GGTTGAGAAAGATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTGGCGCAAAAGATGTGCCTTACGATGAAATAATTAAAGCACTGAACTTGTT                      >  SRR3722139.289920/1‑150 (MQ=60)

                                                                                                                                           GATCGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGctgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgccgtcttctgcttg            >  SRR3722139.342493/1‑84 (MQ=60)

                                                                                                                                              CGCCTGGGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTGGCGCAAAAGATGTGCCTTACGATGAAATAATTAAAGCACTGAACTTGTTACATAGTGCGGGTG        <  SRR3722139.473891/151‑1 (MQ=60)

                                                                                                                                                    GGGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTGGCGCAAAAGATGTGCCTTACGATGAAATAATTAAAGCACTGAACTTGTTACATAGTGCGGGTGTGAAAT  >  SRR3722139.100523/1‑151 (MQ=60)

GACAGCGCCCATCATCACCCAGAGCGTGGAGGTCGATCTGCCAGACGCTACTGAATCACAGGCGGTGAGCAGTAACGATAATCCGCCAGTGATTGTTGAAGTGTCTGGTATTGGTCAGTACACCGTGGTGGTTGAGAAAGATCGCCTGGAGCGTTTACCACCAGAGCAGGTGGTGGCGGAAGTGTCCAGCCGTTTCAAGGCCAACCCGAAAACGGTCTTTCTGATCGGTGGCGCAAAAGATGTGCCTTACGATGAAATAATTAAAGCACTGAACTTGTTACATAGTGCGGGTGTGAAAT  >  NZ_CP009273/771406‑771704

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`