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 I181 R1	159	32.7	1279082	96.9%	1239430	121.0

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%	124.6 / NA	32	Y343C (TAC→TGC)	yajR	MFS transporter
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (16/16); total (16/16)

CTGGCGACTGTCAGCCACACTGCGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAA‑CATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGTAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACGCCGACCACCAGTTGCCAGAACTGCGTTTGCG  >  NZ_CP009273/440966‑441230

cTGGCGCCTGTCAGCCACACTGCGGCCAGCATTGCGCCAGCGAAAAATCCCCCCTGACCGTCAAA‑CATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACAccc                                                                                                                                 <  2:535740/138‑1 (MQ=255)

 tGGCGACTGTCAGCCACACTGCGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAA‑CATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCAt                                                                                                                               >  1:535740/1‑139 (MQ=255)

   gCGACTGTCAGCCACACTGCGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAA‑CATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCg                                                                                                                             >  2:464016/1‑139 (MQ=255)

        tGTCAGCCACACTGCGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAA‑CATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTa                                                                                                                        >  1:101848/1‑139 (MQ=255)

        tGTCAGCCACACTGCGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAA‑CATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTa                                                                                                                        >  2:224406/1‑139 (MQ=255)

                      cGGCCAGCATTGCGCCACCGAGAAATCCCCCCTGCCCGTCAAA‑CATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACctg                                                                                                           <  1:275984/138‑1 (MQ=255)

                            gctttGCCCCAGCGAGAAATCCCCCCTGCCCGTCAAC‑CATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGa                                                                                                    <  2:232370/136‑1 (MQ=255)

                            gCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAA‑CATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGa                                                                                                    >  2:61516/1‑139 (MQ=255)

                            cctttGCCCCAGCGAAAAATCCCCCCTGCCCGTCAAA‑CATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGa                                                                                                    <  2:487200/136‑1 (MQ=255)

                              aTTGCGCCAGCGAGAAATACCCCCTGACCGTCAAA‑CATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCg                                                                                                     >  2:473547/1‑136 (MQ=255)

                              aTTGCGCCAGCGAGAAATACCCCCTGACCGTCAAA‑CATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCg                                                                                                     <  1:473547/136‑1 (MQ=255)

                                  cgcCAGCGAGAAATACCCCCTGACCGTCAAA‑CATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCttt                                                                                              <  1:614135/139‑1 (MQ=255)

                                       gCGAGAAATCCCCCCTGACCGTCAAC‑CATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGa                                                                                         <  1:533264/139‑1 (MQ=255)

                                       gCGAGAAATACCCCCTGACCGTCAAA‑CATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTgg                                                                                                       <  2:9146/125‑1 (MQ=255)

                                       gCGAGAAATACCCCCTGACCGTCAAA‑CATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTgg                                                                                                       >  1:9146/1‑125 (MQ=255)

                                            aaaTCCCCCCGGCCCGTCAAC‑CATGCCGTTAACCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGt                                                                                    <  2:455269/139‑1 (MQ=255)

                                                 cccccTGACC‑TCAAACCATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAggg                                                                               <  2:240537/139‑1 (MQ=255)

                                                     cTGACCGTCAAA‑CATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCagg                                                                           <  2:417573/139‑1 (MQ=255)

                                                      tGACCGTCAAA‑CATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCttt                                                                                              <  1:100959/119‑1 (MQ=255)

                                                      tGACCGTCAAA‑CATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCttt                                                                                              >  2:100959/1‑119 (MQ=255)

                                                      tGACCGTCAAA‑CATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCag                                                                            >  1:240537/1‑137 (MQ=255)

                                                       gACCGTCAAA‑CATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCaggag                                                                         >  1:308096/1‑139 (MQ=255)

                                                            tCAAA‑CATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCtt                                                                    >  2:456878/1‑139 (MQ=255)

                                                                     gCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCaaa                                                            >  1:555710/1‑139 (MQ=255)

                                                                                 gccgccCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCcac                                                 >  1:516941/1‑138 (MQ=255)

                                                                                                gCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACg                                 <  1:480427/139‑1 (MQ=255)

                                                                                                         cacgccaAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACGCCGaccac                         >  1:176895/1‑138 (MQ=255)

                                                                                                           cgccaAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACGCCGACCACCAg                      >  1:142067/1‑139 (MQ=255)

                                                                                                                      tggctggTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACGCCGAccacca                       >  2:192984/1‑127 (MQ=255)

                                                                                                                      tggctggTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACGCCGAccacca                       <  1:192984/127‑1 (MQ=255)

                                                                                                                               gAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACGCCGACCACCAGTTGCCAGAACTGCGTTTgcg  <  1:61516/139‑1 (MQ=255)

                                                                                                                               gAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACGCCGACCACCAGTTGCCAGAACTGCGTTTgcg  <  1:224406/139‑1 (MQ=255)

CTGGCGACTGTCAGCCACACTGCGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAA‑CATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGTAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACGCCGACCACCAGTTGCCAGAACTGCGTTTGCG  >  NZ_CP009273/440966‑441230

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 30 ≤` `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

GGTTCTTTCATGGTACTGGCGACTGTCAGCCACACTGCGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGTAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACGCCGACCACCAGTTGCCAGAACTGCGTTTGCGCGTTCCACAAC  >  NZ_CP009273/440951‑441241

cggagatgtgtataagagacagCTGTCAGCCACACTGCGGCCAGCATTGCGCCAGCGAGAAATCCCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACAC                                                                                                                                              <  SRR3722135.638808/129‑1 (MQ=60)

     TTTCATGGTACTGGCGACTGTCAGCCACACTGCGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATC                                                                                                                                         >  SRR3722135.542827/1‑151 (MQ=60)

            GTACTGGCGACTGTCAGCCACACTGCGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTAC                                                                                                                                  >  SRR3722135.103249/1‑151 (MQ=60)

                              CACCCTGCGGCCAGCATTGCCCCAGCGAGAAATCCCCCCTGCCCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCG                                                                                                                <  SRR3722135.287321/151‑1 (MQ=60)

                                    GCGGCCAGCATTGCGCCACCGAGAAATCCCCCCTGCCCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCT                                                                                                           <  SRR3722135.279967/150‑1 (MQ=60)

                                         CAGCATTGCGCCAGCGAGAAATCCCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTG                                                                                                     <  SRR3722135.479912/151‑1 (MQ=60)

                                           GCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACctgt                                                                                                   >  SRR3722135.9269/1‑147 (MQ=60)

                                                aaagagacagGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTG                                                                                              <  SRR3722135.102351/141‑1 (MQ=60)

                                                GCGCCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTG                                                                                              <  SRR3722135.622156/151‑1 (MQ=60)

                                                     AGCGAGAAATCCCCCCTGACCGTCAACCATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGC                                                                                         <  SRR3722135.540321/151‑1 (MQ=60)

                                                          GAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGG                                                                                      >  SRR3722135.243940/1‑149 (MQ=60)

                                                           AAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGG                                                                                   >  SRR3722135.312503/1‑151 (MQ=60)

                                                                        CCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAAT                                                                      >  SRR3722135.563059/1‑151 (MQ=60)

                                                                                    CCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACA                                                           >  SRR3722135.523809/1‑150 (MQ=60)

                                                                                                            CCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACGCCGACCACC                                   >  SRR3722135.179348/1‑150 (MQ=60)

                                                                                                             CGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACGCCGACCACCAG                                 <  SRR3722135.486881/151‑1 (MQ=60)

                                                                                                              GCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACGCCGACCACCAGT                                >  SRR3722135.144056/1‑151 (MQ=60)

                                                                                                                       agCGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACGCCGACCACCAGTTGCCAGAAC                       <  SRR3722135.195721/149‑1 (MQ=60)

                                                                                                                                            GGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACGCCGACCACCAGTTGCCAGAACTGCGTTTGCGCGTTCCACAAC  <  SRR3722135.227562/151‑1 (MQ=60)

                                                                                                                                            GGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACGCCGACCACCAGTTGCCAGAACTGCGTTTGCGCGTTCCACAAC  <  SRR3722135.62334/151‑1 (MQ=60)

                                                                                                                                             GAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACGCCGACCACCAGTTGCCAGAACTGCGTTTGCGCGTTCCACAAC  >  SRR3722135.235274/1‑150 (MQ=60)

GGTTCTTTCATGGTACTGGCGACTGTCAGCCACACTGCGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGTAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACGCCGACCACCAGTTGCCAGAACTGCGTTTGCGCGTTCCACAAC  >  NZ_CP009273/440951‑441241

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`