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 I175 R1	328	64.7	2582366	96.2%	2484236	120.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	436,326	C→T	A78T (GCT→ACT)	ispA ←	(2E,6E)‑farnesyl diphosphate synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	436,326	0	C	T	89.3%	73.4 / 2.1	28	A78T (GCT→ACT)	ispA	(2E,6E)‑farnesyl diphosphate synthase
Reads supporting (aligned to +/- strand): ref base C (2/1); new base T (11/14); total (13/15)
Fisher's exact test for biased strand distribution p-value = 5.83e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.34e-01

AGAACGCCAGCGTTTGTAAAGCGTCGCCAGCGAGAATCGCGTTTGCTTCGCCAAACTTCACATGGCAGGTTGGCAAACCGCGACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGCGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGCCGAACATATGACCGGTGGCATAAACCAGGAAAGGTCGCAGGCGCTTACCACCTAATAATGCGCCATACTGCA  >  NZ_CP009273/436191‑436451

agaACGCCAGCGTTTGTAAAGCGTCGCCAGCGAGAATCGCGTTTGCTTCGCCAAACTTCACATGGCAGGTTGGCAAACCGCGACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGtgtg                                                                                                                            >  2:548114/1‑139 (MQ=255)

   aCGCCAGCGTTTGTAAAGCGTCGCCAGCGAGAATCGCGTTTGCTTCGCCAAACTTCACATGGCAGGTTGGCAAACCGCGACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGAt                                                                                                                         <  2:106547/139‑1 (MQ=255)

    cGCCAGCGTTTGTAAAGCGTCGCCAGCGAGAATCGCGTTTGCTTCGCCAAACTTCACATGGCAGGTTGGCAAACCGCGACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATa                                                                                                                        >  2:139332/1‑139 (MQ=255)

                       tCGCCAGCGAGAATCGCGTTTGCTTCGCCAAACTTCACATGGCAGGTTGGCAAACCGCGACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATACCCTCAACGGCGGCAGCgg                                                                                                     >  2:363369/1‑139 (MQ=255)

                       tCGCCAGCGAGAATCGCGTTTGCTTCGCCAAACTTCACATGGCAGGTTGGCAAACCGCGACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATACACTCAACGGCGGCAGCgg                                                                                                     >  2:744464/1‑139 (MQ=255)

                       tCGCCAGCGAGAATCGCGTTTGCTTCGCCAAACTTCACATGGCAGGTTGGCAAACCGCGACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATACACTCAACGGCGGCAGCgg                                                                                                     >  1:954353/1‑139 (MQ=255)

                        cGCCAGCGAGAATCGCGTTTGCTTCGCCAAACTTCACATGGCAGGTTGGCAAACCGCGACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATACACTCAACGGCGGCAGCggg                                                                                                    >  1:538519/1‑139 (MQ=255)

                                             cTTCGCCAAACTTCACATGGCAGGTTGGCAAACCGCGACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCt                                                                               <  1:231387/139‑1 (MQ=255)

                                                  ccAAACTTCACATGGCAGGTTGGCAAACCGCGACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGc                                                                          >  2:36634/1‑139 (MQ=255)

                                                   cAAACTTCACATGGCAGGTTGGCAAACCGCGACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGcc                                                                         <  2:59850/139‑1 (MQ=255)

                                                      aCTTCACATGGCAGGTTGGCAAACCGCGACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGCCGaa                                                                      <  1:652602/139‑1 (MQ=255)

                                                                 cAGGTTGGCAAACCGCGACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGCCGAACATATGACCgg                                                           <  2:206191/139‑1 (MQ=255)

                                                                    gTTGGCAAACCGCGACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGcc                                                                         <  1:1254309/122‑1 (MQ=255)

                                                                    gTTGGCAAACCGCGACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGcc                                                                         >  2:1254309/1‑122 (MQ=255)

                                                                    gTTGGCAAACCGCGACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGCGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGCCGAACATATGACCGGTgg                                                        >  1:1006983/1‑139 (MQ=255)

                                                                       ggCAAACCGCGACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGCCGAACATATGACCGGTGGCa                                                      <  2:219642/138‑1 (MQ=255)

                                                                                  aCGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGCCGAACATATGACCGGTGGCATAAACCAGGaaa                                          <  1:363369/139‑1 (MQ=255)

                                                                                        aTCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGCGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGCCGAACATATGACCGGTGGCATAAACCAGGAAAGGTCg                                     >  2:262967/1‑138 (MQ=255)

                                                                                                 atcCATTGCTGGTAAATCATCATGAATTAATGAGTAAGTGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGCCGAACATATGACCGGTGGCATAAACCAGGAAAGGTCGCAGGCGCTTa                           <  2:320022/139‑1 (MQ=255)

                                                                                                 atcCATTGCCGGTAAATCGTCATGAATTAATGAGTAAGTGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGCCGAACATATGACCGGTGGCATAAACCAGGAAAGGTCGCAGGCGCTTa                           <  2:935179/139‑1 (MQ=255)

                                                                                                 atcCATTGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGCCGAACATATGACCGGTGGCATAAACCAGGAAAGGTCGCAGGCGCTTa                           <  2:1273467/139‑1 (MQ=255)

                                                                                                  tcCATTGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGCCGAACATATGACCGGTGGCATAAACCAGGAAAGGTCGCAGGCGCTTac                          <  1:611467/139‑1 (MQ=255)

                                                                                                      ttGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATACACTCAACGGCGGCAGCGGGGGCGTCCAGCGTGTTTGTGCTAACGCCGAACATATGACCGGTGGCATAAACCAGGAAAGGTCGCAGGCGCTTaccacc                      >  2:1033259/1‑139 (MQ=255)

                                                                                                       tGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGCCGAACATATGACCGGTGGCATAAACCAGGAAAGGTCGCAGGCGCTTaccacc                      >  2:291047/1‑138 (MQ=255)

                                                                                                       tGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGCCGAACATATGACCGGTGGCATAAACCAGGAAAGGTCGCAGGCGCTTaccacc                      >  1:901175/1‑138 (MQ=255)

                                                                                                       tGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGCCGAACATATGACCGGTGGCATAAACCAGGAAAGGTCGCAGGCGCTTaccacc                      >  1:596330/1‑138 (MQ=255)

                                                                                                           ggTAAATCATCATGAATTAATGAGTAAGTGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGCCGAACATATGACCGGTGGCATAAACCAGGAAAGGTCGCAGGCGCTTACCACCtaata                 <  2:954353/139‑1 (MQ=255)

                                                                                                                   atcatGAATTAATGAGTAAGCGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGCCGAACATATGACCGGTGGCATAAACCAGGAAAGGTCGCAGGCGCTTACCACCTAATAATGCGCCa         <  2:1006983/139‑1 (MQ=255)

                                                                                                                          aTTAATGAGTAAGTGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGCCGAACATATGACCGGTGGCATAAACCAGGAAAGGTCGCAGGCGCTTACCACCTAATAATGCGCCATACTGCa  <  2:330771/139‑1 (MQ=255)

AGAACGCCAGCGTTTGTAAAGCGTCGCCAGCGAGAATCGCGTTTGCTTCGCCAAACTTCACATGGCAGGTTGGCAAACCGCGACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGCGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGCCGAACATATGACCGGTGGCATAAACCAGGAAAGGTCGCAGGCGCTTACCACCTAATAATGCGCCATACTGCA  >  NZ_CP009273/436191‑436451

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 20 ≤` `ATCG/ATCG` `< 35 ≤` `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

GCTTAAAATCGAGAACGCCAGCGTTTGTAAAGCGTCGCCAGCGAGAATCGCGTTTGCTTCGCCAAACTTCACATGGCAGGTTGGCAAACCGCGACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGCGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGCCGAACATATGACCGGTGGCATAAACCAGGAAAGGTCGCAGGCGCTTACCACCTAATAATGCGCCATACTGCATGGTTTCGACCACGGGAGTGTTCT  >  NZ_CP009273/436180‑436475

GCTTAAAATCGAGAACGCCAGCGTTTGTAAAGCGTCGCCAGCGAGAATCGCGTTTGCTTCGCCAAACTTCACATGGCAGGTTGGCAAACCGCGACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGG                                                                                                                                                   >  SRR3722129.383618/1‑151 (MQ=60)

   aagcagaagacggcatacgagattcgccttagtctcgtgggctcggagatgtgtataagagacagTCACATGGCAGGTTGGCAAACCGCGACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATA                                                                                                                                                <  SRR3722129.275794/86‑1 (MQ=60)

    gggctcggagatgtgtataagagacagGCGTCGCCAGCGAGAATCGCGTTTGCTTCGCCAAACTTCACATGGCAGGTTGGCAAACCGCGACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATAC                                                                                                                                               <  SRR3722129.841168/124‑1 (MQ=60)

    AAAATCGAGAACGCCAGCGTTTGTAAAGCGTCGCCAGCGAGAATCGCGTTTGCTTCGCCAAACTTCACATGGCAGGTTGGCAAACCGCGACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATAC                                                                                                                                               <  SRR3722129.863725/151‑1 (MQ=60)

    AAAATCGAGAACGCCAGCGTTTGTAAAGCGTCGCCAGCGAGAATCGCGTTTGCTTCGCCAAACTTCACATGGCAGGTTGGCAAACCGCGACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATA                                                                                                                                                <  SRR3722129.386379/150‑1 (MQ=60)

    AAAATCGAGAACGCCAGCGTTTGTAAAGCGTCGCCAGCGAGAATCGCGTTTGCTTCGCCAAACTTCACATGGCAGGTTGGCAAACCGCGACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGCGTGGATAC                                                                                                                                               <  SRR3722129.573022/151‑1 (MQ=60)

         CGAGAACGCCAGCGTTTGTAAAGCGTCGCCAGCGAGAATCGCGTTTGCTTCGCCAAACTTCACATGGCAGGTTGGCAAACCGCGACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATACACTC                                                                                                                                           <  SRR3722129.1077245/150‑1 (MQ=60)

               CGCCAGCGTTTGTAAAGCGTCGCCAGCGAGAATCGCGTTTGCTTCGCCAAACTTCACATGGCAGGTTGGCAAACCGCGACGCAGATCGTCATCATCCAGTGCCGGAAAATCATCATGAATTAATGAGTAAGGGTGGATAGACTGAACGGCG                                                                                                                                    >  SRR3722129.537532/1‑151 (MQ=60)

                       TTTGTAAAGCGTCGCCAGCGAGAATCGCGTTTGCTTCGCCAAACTTCACATGGCAGGTTGGCAAACCGCGACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATACACTCAACGGCGGCAGCGGG                                                                                                                            >  SRR3722129.967838/1‑151 (MQ=60)

                        TTGTAAAGCGTCGCCAGCGAGAATCGCGTTTGCTTCGCCAAACTTCACATGGCAGGTTGGCAAACCGCGACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATACACTCAACGGCGGCAGCGGGT                                                                                                                           >  SRR3722129.546396/1‑151 (MQ=60)

                                                       GCTTCGCCAAACTTCACATGGCAGGTTGGCAAACCGCGACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGCCGAACA                                                                                            <  SRR3722129.234679/151‑1 (MQ=60)

                                                             gagacagTCACATGGCAGGTTGGCAAACCGCGACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGCCGAACATATGAC                                                                                      <  SRR3722129.1271755/144‑1 (MQ=60)

                                                                AACTTCACATGGCAGGTTGGCAAACCGCGACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGCCGAACATATGACCGG                                                                                   <  SRR3722129.662321/151‑1 (MQ=60)

                                                                    TCACATGGCAGGTTGGCAAACCGCGACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGCGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGCCGAACATATGACCGGTGGC                                                                               >  SRR3722129.1021168/1‑151 (MQ=60)

                                                                                agaagacggcatacgagattcgccttagtctcgtgggctcggagatgtgtataagagacagGTAAGTGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGCCGAACATATGACCGGTGGCATAAACCAGGAA                                                                   <  SRR3722129.1003171/90‑1 (MQ=60)

                                                                                            GACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGCCGAACATATGACCGGTGGCATAAACCAGGAAAGGTCGCAGGCG                                                       <  SRR3722129.368623/151‑1 (MQ=60)

                                                                                                       TCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGCCGAACATATGACCGGTGGCATAAACCAGGAAAGGTCGCAGGCGCTTACCACCT                                             >  SRR3722129.913953/1‑150 (MQ=60)

                                                                                                       TCATAATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGCCGAACATATGACCGGTGGCATAAACCAGGAAAGGTCGCAGGCGCTTACCACCT                                             >  SRR3722129.605232/1‑150 (MQ=60)

                                                                                                            ATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGTGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGCCGAACATATGACCGGTGGCATAAACCAGGAAAGGTCGCAGGCGCTTACCACCTAATAAT                                       <  SRR3722129.620568/151‑1 (MQ=60)

                                                                                                                                           GAGTAAGCGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGCCGAACATATGACCGGTGGCATAAACCAGGAAAGGTCGCAGGCGCTTACCACCTAATAATGCGCCATACTGCATGGTTTCGACCACGGG          >  SRR3722129.405400/1‑149 (MQ=60)

                                                                                                                                                 GTGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGCCGAACATATGACCGGTGGCATAAACCAGGAAAGGTCGCAGGCGCTTACCACCTAATAATGCGCCATACTGCATGGTTTCGACCACGGGAGTGTTCT  >  SRR3722129.1227821/1‑151 (MQ=60)

GCTTAAAATCGAGAACGCCAGCGTTTGTAAAGCGTCGCCAGCGAGAATCGCGTTTGCTTCGCCAAACTTCACATGGCAGGTTGGCAAACCGCGACGCAGATCGTCATCATCCATTGCCGGTAAATCATCATGAATTAATGAGTAAGCGTGGATACACTCAACGGCGGCAGCGGGTGCGTCCAGCGTGTTTGTGCTAACGCCGAACATATGACCGGTGGCATAAACCAGGAAAGGTCGCAGGCGCTTACCACCTAATAATGCGCCATACTGCATGGTTTCGACCACGGGAGTGTTCT  >  NZ_CP009273/436180‑436475

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 29 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`