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 I177 R1	141	27.5	996908	97.7%	973979	124.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	441,095	T→C	Y343C (TAC→TGC)	yajR ←	MFS transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	441,095	0	T	C	100.0%	96.7 / NA	26	Y343C (TAC→TGC)	yajR	MFS transporter
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (13/13); total (13/13)

GCGACTGTCAGCCACACTGCGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGTAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACGCCGACCACCAGTTGCCAGAACTGC  >  NZ_CP009273/440969‑441223

gCGACTGTCAGCCCCACTGCGGCCAGAATTGCGCCGGCGAGAAATCCCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCAt                                                                                                                        <  1:483427/137‑1 (MQ=255)

    cTGTCACCCACACTGCGGCCAGCATTGCGCCGGCGAAAAATCCCCCCTGCCCGTCAACCATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGt                                                                                                                  <  2:153693/139‑1 (MQ=255)

       tCAGCCACACTGCGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTAcc                                                                                                               >  1:307195/1‑139 (MQ=255)

               ccTGCGGCCAGCTTTGCGCCGGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAAc                                                                                                       <  1:409697/138‑1 (MQ=255)

               acTGCGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAAc                                                                                                       >  1:131134/1‑139 (MQ=255)

                   cGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACAccc                                                                                                                          >  2:431984/1‑116 (MQ=255)

                   cGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACAccc                                                                                                                          <  1:431984/116‑1 (MQ=255)

                   cGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACctgc                                                                                                   >  1:359055/1‑139 (MQ=255)

                        aGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGc                                                                                               >  1:139745/1‑138 (MQ=255)

                        aGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGc                                                                                               >  2:490474/1‑138 (MQ=255)

                              gcgcCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCtt                                                                                        >  1:95436/1‑139 (MQ=255)

                                    gCGAAAAACCCCCCCGGCCCGTCAACCATGCCGTTAACCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGa                                                                                  <  2:95436/139‑1 (MQ=255)

                                         aaaTCCCCCCTGACCTCCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGt                                                                             <  2:307195/139‑1 (MQ=255)

                                         aaaTACCCCCAGACCGTCAACCAGGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGt                                                                             <  2:131134/139‑1 (MQ=255)

                                                   tGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCttt                                                                                       <  1:198626/119‑1 (MQ=255)

                                                   tGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCttt                                                                                       >  2:198626/1‑119 (MQ=255)

                                                       cGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGc                                                               >  1:134436/1‑139 (MQ=255)

                                                                 gCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTa                                                                                                                 >  2:180366/1‑79 (MQ=255)

                                                                 gCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTa                                                                                                                 <  1:180366/79‑1 (MQ=255)

                                                                       aaTCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTaaa                                                <  2:439005/138‑1 (MQ=255)

                                                                           cAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCca                                           <  2:218280/139‑1 (MQ=255)

                                                                                          ccGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCa                            <  1:326035/139‑1 (MQ=255)

                                                                                                                    gctggTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACGCCGACCACCAGTTGCCAGAACTGc  >  1:390191/1‑139 (MQ=255)

                                                                                                                    gctggTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACGCCGACCACCAGTTGCCAGAACTGc  >  2:238392/1‑139 (MQ=255)

                                                                                                                        gtggAGCAAACACCCATCGCCGTACCTTTGTAACctg                                                                                                    >  2:152477/1‑37 (MQ=255)

                                                                                                                        gtggAGCAAACACCCATCGCCGTACCTTTGTAACctg                                                                                                    <  1:152477/37‑1 (MQ=255)

GCGACTGTCAGCCACACTGCGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGTAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACGCCGACCACCAGTTGCCAGAACTGC  >  NZ_CP009273/440969‑441223

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 25 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

ACTGGCGACTGTCAGCCACACTGCGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGTAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACGCCGACCACCAGTTGCCAGAACTGCGTTTGCGCGTTCCACAACAC  >  NZ_CP009273/440965‑441243

tataagacacagCAGCCACCCTGCGGCCAGCATTGCGCCAGCGAGAAATCCCCCCTGCCCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACC                                                                                                                                   <  SRR3722131.436646/138‑1 (MQ=60)

ACTGGCGACTGTCAGCCACACTGCGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCT                                                                                                                                  >  SRR3722131.310700/1‑151 (MQ=60)

   GGCGACTGTCAGCCCCACTGCGGCCAGAATTGCGCCGGCGAGAAATCCCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTT                                                                                                                                 <  SRR3722131.488612/149‑1 (MQ=60)

        CTGTCAGCCACACTGCGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACC                                                                                                                          >  SRR3722131.132589/1‑151 (MQ=60)

         acgagctctagtccggtctcgggggttcggagatgttaaaaagagacagcggaCAAACATGCCGTTAACCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACC                                                                                                                          <  SRR3722131.182454/97‑1 (MQ=60)

            CAGCCACACTGCGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCT                                                                                                                      >  SRR3722131.363076/1‑151 (MQ=60)

                 ACACTGCGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCG                                                                                                                  >  SRR3722131.141312/1‑150 (MQ=60)

                  CCCTGCGGCCAGCTTTGCGCCGGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGAC                                                                                                                <  SRR3722131.414129/151‑1 (MQ=60)

                     atagatagatcactttttttttttttcaagcagaagacggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCT                                                                                                             <  SRR3722131.154253/59‑1 (MQ=60)

                       CGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTT                                                                                                           >  SRR3722131.96493/1‑151 (MQ=60)

                                  aaagagacagGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTG                                                                                                <  SRR3722131.200927/141‑1 (MQ=60)

                                                TACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCT                                                                                  >  SRR3722131.135927/1‑151 (MQ=60)

                                                                                             ACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACGCCGACCACC                                     <  SRR3722131.329713/151‑1 (MQ=60)

                                                                                                             CCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACGCCGACCACCAGTTGCCAGAACTGCG                     >  SRR3722131.394456/1‑151 (MQ=60)

                                                                                                                                AGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACGCCGACCACCAGTTGCCAGAACTGCGTTTGCGCGTTCCACAACAC  >  SRR3722131.280833/1‑151 (MQ=60)

ACTGGCGACTGTCAGCCACACTGCGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGTAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACGCCGACCACCAGTTGCCAGAACTGCGTTTGCGCGTTCCACAACAC  >  NZ_CP009273/440965‑441243

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`