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	453,525	T→A	I215N (ATC→AAC)	clpX →	ATP‑dependent protease ATP‑binding subunit ClpX

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	453,525	0	T	A	100.0%	99.2 / NA	25	I215N (ATC→AAC)	clpX	ATP‑dependent protease ATP‑binding subunit ClpX
Reads supporting (aligned to +/- strand): ref base T (0/0); new base A (11/14); total (11/14)

CAGAAAGCACAGCGTGGTATTGTCTACATCGATGAAATCGACAAGATTTCTCGTAAGTCAGACAACCCGTCCATTACCCGAGACGTTTCCGGTGAAGGCGTACAGCAGGCACTGTTGAAACTGATCGAAGGTACGGTAGCTGCTGTTCCACCGCAAGGTGGGCGTAAACATCCGCAGCAGGAATTCTTGCAGGTTGATACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCC  >  NZ_CP009273/453401‑453658

cAGAAAGCACAGCGTGGTATTGTCTACATCGATGAAATCGACAAGATTTCTCGTAAGTCAGACAACCCGTCCATTACCCGAGACGTTTCCGGTGAAGGCGTACAGCAGGCACTGTTGAAACTGAACGAAGGt                                                                                                                                <  2:591988/132‑1 (MQ=255)

cAGAAAGCACAGCGTGGTATTGTCTACATCGATGAAATCGACAAGATTTCTCGTAAGTCAGACAACCCGTCCATTACCCGAGACGTTTCCGGTGAAGGCGTACAGCAGGCACTGTTGAAACTGAACGAAGGt                                                                                                                                >  1:591988/1‑132 (MQ=255)

cAGAAAGCACAGCGTGGTATTGTCTACATCGATGAAATCGACAAGATTTCTCGTAAGTCAGACAACCCGTCCATTACCCGAGACGTTTCCGGTGAAGGCGTACAGCAGGCACTGTTGAAACTGAACGAAGGTACGGTa                                                                                                                          <  1:350630/138‑1 (MQ=255)

 aGAAAGCACAGCGTGGTATTGTCTACATCGATGAAATCGACAAGATTTCTCGTAAGTCAGACAACCCGTCCATTACCCGAGACGTTTCCGGTGAAGGCGTACAGCAGGCACTGTTGAAACTGAACGAAGGTACGGTAgc                                                                                                                        <  1:228923/139‑1 (MQ=255)

         caGCGTGGTATTGTCTACATCGATGAAATCGACAAGATTTCTCGTAAGTCAGACAACCCGTCCATTACCCGAGACGTTTCCGGTGAAGGCGTACAGCAGGCACTGTTGAAACTGAACGAAGGTACGGTAGCTGCTGTTc                                                                                                                <  1:413741/139‑1 (MQ=255)

            cGTGGTATTGTCTACATCGATGAAATCGACAAGATTTCTCGTAAGTCAGACAACCCGTCCATTACCCGAGACGTTTCCGGTGAAGGCGTACAGCAGGCACTGTTGAAACTGAACGAAGGTACGGTAGCTGCTGTTCCAc                                                                                                             >  1:386801/1‑139 (MQ=255)

                           aTCGATGAAATCGACAAGATTTCTCGTAAGTCAGACAACCCGTCCATTACCCGAGACGTTTCCGGTGAAGGCGTACAGCAGGCACTGTTGAAACTGAACGAAGGTACGGTAGCTGCTGTTCCACCGCAAGGTGGGCGt                                                                                               >  2:20225/1‑138 (MQ=255)

                           aTCGATGAAATCGACAAGATTTCTCGTAAGTCAGACAACCCGTCCATTACCCGAGACGTTTCCGGTGAAGGCGTACAGCAGGCACTGTTGAAACTGAACGAAGGTACGGTAGCTGCTGTTCCACCGCAAGGAGGGCGt                                                                                               >  2:337761/1‑138 (MQ=255)

                                tGAAATCGACAAGATTTCTCGTAAGTCAGACAACCCGTCCATTACCCGAGACGTTTCCGGTGAAGGCGTACAGCAGGCACTGTTGAAACTGAACGAAGGTACGGTAGCTGCTGTTCCACCGCAAGGTGGGCGTAAACAt                                                                                         >  1:629930/1‑139 (MQ=255)

                                   aaTCGACAAGATTTCTCGTAAGTCAGACAACCCGTCCATTACCCGAGACGTTTCCGGTGAAGGCGTACAGCAGGCACTGTTGAAACTGAACGAAGGTACGGTAGCTGCTGTTCCACCGCAAGGTGGGCGTAAACATCCg                                                                                      <  1:588187/139‑1 (MQ=255)

                                                    gTAAGTCAGACAACCCGTCCATTACCCGAGACGTTTCCGGTGAAGGCGTACAGCAGGCACTGTTGAAACTGAACGAAGGTACGGTAGCTGCTGTTCCACCGCAAGGTGGGCGTAAACATCCGCAGCAGGAATTCTTg                                                                       <  1:98348/137‑1 (MQ=255)

                                                    gTAAGTCAGACAACCCGTCCATTACCCGAGACGTTTCCGGTGAAGGCGTACAGCAGGCACTGTTGAAACTGAACGAAGGTACGGTAGCTGCTGTTCCACCGCAAGGTGGGCGTAAACATCCGCAGCAGGAATTCTTg                                                                       <  2:621075/137‑1 (MQ=255)

                                                           aGACAACCCGTCCATTACCCGAGACGTTTCCGGTGTAGGCGTACAGCAGGCACTGTTGAAACTGAACGACGGTACGGTAGCTGCTGTTCCACCGCAAGGTGGGCGTAATCATCCGCAGCAGGAATTCTTGCAGGTTGAt                                                              <  2:428765/139‑1 (MQ=255)

                                                           aGACAACCCGTCCATTACCCGAGACGTTTCCGGTGAAGGCGTACAGCAGGCACTGTTGAAACTGAACGAAGGTACGGTAGCTGCTGTTCCACCGCAAGGTGGGCGTAAACATCCGCAGCAGGAATTCTTGCAGGTTGa                                                               <  1:206600/138‑1 (MQ=255)

                                                              cAACCCGTCCATTACCCGAGACGTTTCCGGTGAAGGCGTACAGCAGGCACTGTTGGAACTGAACGAAGGTACGGTAGCTGCTGTTCCACCGCAAGGTGGGCGTAAACATCCGCAGCAGGAATTCTTg                                                                       >  1:114279/1‑127 (MQ=255)

                                                              cAACCCGTCCATTACCCGAGACGTTTCCGGTGAAGGCGTACAGCAGGCACTGTTGGAACTGAACGAAGGTACGGTAGCTGCTGTTCCACCGCAAGGTGGGCGTAAACATCCGCAGCAGGAATTCTTg                                                                       <  2:114279/127‑1 (MQ=255)

                                                                      ccATTACCCGAGACGTTTCCGGTGAAGGCGTACAGCAGGCACTGTTGAAACTGAACGAAGGTACGGTAGCTGCTGTTCCACCGCAAgg                                                                                                      <  2:114922/88‑1 (MQ=255)

                                                                      ccATTACCCGAGACGTTTCCGGTGAAGGCGTACAGCAGGCACTGTTGAAACTGAACGAAGGTACGGTAGCTGCTGTTCCACCGCAAgg                                                                                                      >  1:114922/1‑88 (MQ=255)

                                                                            cccGAGACGTTTCCGGTGAAGGCGTACAGCAGGCACTGTTGAAACTGAACGAAGGTACGGTAGCTGCTGTTCCACCGCAAGGTGGGCGTAAACATCCGCAGCAGGAATTCTTGCAGGTTGATACCTCTAAGATCCTGtt                                             >  2:449681/1‑139 (MQ=255)

                                                                                           gTGAAGGCGTACAGCAGGCACTGTTGAAACTGAACGAAGGTACGGTAGCTGCTGTTCCACCGCAAGGTGGGCGTAAACATCCGCAGCAGGAATTCTTGCAGGTTGATACCTCTAAGATCCTGTTTATTTGTGGCGGTGc                              >  2:4664/1‑139 (MQ=255)

                                                                                                               cTGTTGAAACTGAACGAAGGTACGGTAGCTGCTGTTCCACCGCAAGGTGGGCGTAAACATCCGCAGCAGGAATTCTTGCAGGTTGATACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAg          <  1:20225/139‑1 (MQ=255)

                                                                                                                 gTTGAAACTGAACGAAGGTACGGTAGCTGCTGTTCCACCGCAAGGTGGGCGTAAACATCCGCAGCAGGAATTCTTGCAGGTTGATACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGt         >  2:589244/1‑138 (MQ=255)

                                                                                                                  ttGAAACTGAACGAAGGTACGGTAGCTGCTGTTCCACCGCAAGGTGGGCGTAAACATCCGCAGCAGGAATTCTTGCAGGTTGATACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGGTAAAGTGa       >  2:370751/1‑139 (MQ=255)

                                                                                                                  ttGAAACTGAACGAAGGTACGGTAGCTGCTGTTCCACCGCAAGGTGGGCGTAAACATCCGCAGCAGGAATTCTTGCAGGTTGATACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTg        <  1:399407/138‑1 (MQ=255)

                                                                                                                       aCTGAACGAAGGTACGGTAGCTGCTGTTCCACCGCAAGGTGGGCGTAAACATCCGCAGCAGGAATTCTTGCAGGTTGATACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTcc  <  2:381498/139‑1 (MQ=255)

CAGAAAGCACAGCGTGGTATTGTCTACATCGATGAAATCGACAAGATTTCTCGTAAGTCAGACAACCCGTCCATTACCCGAGACGTTTCCGGTGAAGGCGTACAGCAGGCACTGTTGAAACTGATCGAAGGTACGGTAGCTGCTGTTCCACCGCAAGGTGGGCGTAAACATCCGCAGCAGGAATTCTTGCAGGTTGATACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCC  >  NZ_CP009273/453401‑453658

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 28 ≤` `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

ACTACGATGTCCAGAAAGCACAGCGTGGTATTGTCTACATCGATGAAATCGACAAGATTTCTCGTAAGTCAGACAACCCGTCCATTACCCGAGACGTTTCCGGTGAAGGCGTACAGCAGGCACTGTTGAAACTGATCGAAGGTACGGTAGCTGCTGTTCCACCGCAAGGTGGGCGTAAACATCCGCAGCAGGAATTCTTGCAGGTTGATACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACC  >  NZ_CP009273/453390‑453673

ACTACGATGTCCAGAAAGCACAGCGTGGTATTGTCTACATCGATGAAATCGACAAGATTTCTCGTAAGTCAGACAACCCGTCCATTACCCGAGACGTTTCCGGTGAAGGCGTACAGCAGGCACTGTTGAAACTGAACGAAGGTACGGTAGC                                                                                                                                       >  SRR3722135.599726/1‑151 (MQ=60)

          CCAGAAAGCACAGCGTGGTATTGTCTACATCGATGAAATCGACAAGATTTCTCGTAAGTCAGACAACCCGTCCATTACCCGAGACGTTTCCGGTGAAGGCGTACAGCAGGCACTGTTGAAACTGAACGAAGGTACGGTAGCTGCTGTTCC                                                                                                                              <  SRR3722135.355585/150‑1 (MQ=60)

           CAGAAAGCACAGCGTGGTATTGTCTACATCGATGAAATCGACAAGATTTCTCGTAAGTCAGACAACCCGTCCATTACCCGAGACGTTTCCGGTGAAGGCGTACAGCAGGCACTGTTGAAACTGAACGAAGGTACGGTAGCTGCTGTTCCAC                                                                                                                            <  SRR3722135.232128/151‑1 (MQ=60)

            AGAAAGCACAGCGTGGTATTGTCTACATCGATGAAATCGACAAGATTTCTCGTAAGTCAGACAACCCGTCCATTACCCGAGACGTTTCCGGTGAAGGCGTACAGCAGGCACTGTTGAAACTGAACGAAGGTACGGTAGCTGCTGTTCCACC                                                                                                                           >  SRR3722135.392187/1‑151 (MQ=60)

                   ACAGCGTGGTATTGTCTACATCGATGAAATCGACAAGATTTCTCGTAAGTCAGACAACCCGTCCATTACCCGAGACGTTTCCGGTGAAGGCGTACAGCAGGCACTGTTGAAACTGAACGAAGGTACGGTAGCTGCTGTTCCACCGCAAGGT                                                                                                                    <  SRR3722135.419431/151‑1 (MQ=60)

                                GTCTACATCGATGAAATCGACAAGATTTCTCGTAAGTCAGACAACCCGTCCATTACCCGAGACGTTTCCGGTGAAGGCGTACAGCAGGCACTGTTGAAACTGAACGAAGGTACGGTAGCTGCTGTTCCACCGCAAGGTGGGCGTAAACATC                                                                                                       >  SRR3722135.638134/1‑151 (MQ=60)

                                             AAATCGACAAGATTTCTCGTAAGTCAGACAACCCGTCCATTACCCGAGACGTTTCCGGTGAAGGCGTACAGCAGGCACTGTTGAAACTGAACGAAGGTACGGTAGCTGCTGTTCCACCGCAAGGTGGGCGTAAACATCCGCAGCAGGAATT                                                                                          <  SRR3722135.595892/151‑1 (MQ=60)

                                                              CGTAAGTCAGACAACCCGTCCATTACCCGAGACGTTTCCGGTGAAGGCGTACAGCAGGCACTGTTGGAACTGAACGAAGGTACGGTAGCTGCTGTTCCACCGCAAGGTGGGCGTAAACATCCGCAGCAGGAATTCTTGCAGGTTGATACCT                                                                         >  SRR3722135.115832/1‑151 (MQ=60)

                                                              CGTAAGTCAGACAACCCGTCCATTACCCGAGACGTTTCCGGTGAAGGCGTACAGCAGGCACTGTTGAAACTGAACGAAGGTACGGTAGCTGCTGTTCCACCGCAAGGTGGGCGTAAACATCCGCAGCAGGAATTCTTGCAGGTTGATAC                                                                           <  SRR3722135.99703/149‑1 (MQ=60)

                                                                     CAGACAACCCGTCCATTACCCGAGACGTTTCCGGTGAAGGCGTACAGCAGGCACTGTTGAAACTGAACGAAGGTACGGTAGCTGCTGTTCCACCGCAAGGTGGGCGTAAACATCCGCAGCAGGAATTCTTGCAGGTTGATACCTCTAAGA                                                                   <  SRR3722135.209496/150‑1 (MQ=60)

                                                                      AGACAACCCGTCCATTACCCGAGACGTTTCCGGTGAAGGCGTACAGCAGGCACTGTTGAAACTGAACGAAGGTACGGTAGCTGCTGTTCCACCGCAAGGTGGGCGTAAACctgtctcttatacacatctccgagcccacgagaccgtact                                                                  >  SRR3722135.116485/1‑110 (MQ=60)

                                                                                                          gatgtgtataagagacagGTTGAAACTGAACGAAGGTACGGTAGCTGCTGTTCCACCGCAAGGTGGGCGTAAACATCCGCAGCAGGAATTCTTGCAGGTTGATACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGAT                             <  SRR3722135.225226/133‑1 (MQ=60)

                                                                                                                         ACTGTTGAAACTGAACGAAGGTACGGTAGCTGCTGTTCCACCGCAAGGTGGGCGTAAACATCCGCAGCAGGAATTCTTGCAGGTTGATACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCAC              <  SRR3722135.20487/151‑1 (MQ=60)

                                                                                                                            GTTGAAACTGAACGAAGGTACGGTAGCTGCTGTTCCACCGCAAGGTGGGCGTAAACATCCGCAGCAGGAATTCTTGCAGGTTGATACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCG            <  SRR3722135.404940/150‑1 (MQ=60)

                                                                                                                                     GAACGAAGGTACGGTAGCTGCTGTTCCACCGCAAGGTGGGCGTAAACATCCGCAGCAGGAATTCTTGCAGGTTGATACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACC  <  SRR3722135.462996/151‑1 (MQ=60)

                                                                                                                                     GAACGAAGGTACGGTAGCTGCTGTTCCACCGCAAGGTGGGCGTAAACATCCGCAGCAGGAATTCTTGCAGGTTGATACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAAC   <  SRR3722135.342553/150‑1 (MQ=60)

                                                                                                                                     GAACGAAGGTACGGTAGCTGCTGTTCCACCGCAAGGTGGGCGTAAACATCCGCAGCAGGAATTCTTGCAGGTTGATACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAAC   <  SRR3722135.455768/150‑1 (MQ=60)

ACTACGATGTCCAGAAAGCACAGCGTGGTATTGTCTACATCGATGAAATCGACAAGATTTCTCGTAAGTCAGACAACCCGTCCATTACCCGAGACGTTTCCGGTGAAGGCGTACAGCAGGCACTGTTGAAACTGATCGAAGGTACGGTAGCTGCTGTTCCACCGCAAGGTGGGCGTAAACATCCGCAGCAGGAATTCTTGCAGGTTGATACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACC  >  NZ_CP009273/453390‑453673

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`