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 F1 I1 R1	748	32.0	1685426	92.6%	1560704	103.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,664,986	C→T	275 (TAG→TAA)	gadX ←	acid resistance regulon transcriptional activator, autoactivator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,664,986	0	C	T	100.0%	160.5 / NA	50	275 (TAG→TAA)	gadX	acid resistance regulon transcriptional activator, autoactivator
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (26/24); total (26/24)

AACTTACTGAGAGCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTCTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATACTCTGTGGGCGTCATCCCATA  >  NC_000913/3664859‑3665117

aaCTTACTGAGAGCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTAt                                                                                                                          >  2:703713/1‑139 (MQ=255)

   ttACTGAGAGCACAAAGTGTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTAttcc                                                                                                                       <  1:563980/139‑1 (MQ=255)

            gCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGa                                                                                                              >  1:301308/1‑139 (MQ=255)

             cacaAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGaa                                                                                                             >  1:414708/1‑139 (MQ=255)

             cacaAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGaa                                                                                                             >  1:452537/1‑139 (MQ=255)

                                    ggAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTccc                                                                                      <  1:703713/139‑1 (MQ=255)

                                       gtgtTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTg                                                                                   <  2:452537/139‑1 (MQ=255)

                                         gtTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTgcg                                                                                 <  2:17905/139‑1 (MQ=255)

                                            ataACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGcaa                                                                              <  2:676527/139‑1 (MQ=255)

                                                  gTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGa                                                                                                              >  1:280851/1‑101 (MQ=255)

                                                  gTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGa                                                                                                              <  2:280851/101‑1 (MQ=255)

                                                    ttattaTTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTAGAATCTTAttccttcc                                                                                                                   <  2:559931/94‑1 (MQ=255)

                                                    ttattaGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTAttccttcc                                                                                                                   >  1:559931/1‑94 (MQ=255)

                                                    ttattaGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACtt                                                                      >  1:637156/1‑139 (MQ=255)

                                                               gagaCGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTTCGCAACAATACTTgccgc                                                                 >  1:774844/1‑133 (MQ=255)

                                                               gagaCGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTgccgc                                                                 <  2:774844/133‑1 (MQ=255)

                                                               gagaCGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTc                                                           >  1:645128/1‑139 (MQ=255)

                                                                  aCGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACg                                                        <  1:272204/139‑1 (MQ=255)

                                                                    ggCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTgc                                                                                  <  2:440909/111‑1 (MQ=255)

                                                                    ggCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTgc                                                                                  >  1:440909/1‑111 (MQ=255)

                                                                    ggCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGt                                                      >  2:256348/1‑139 (MQ=255)

                                                                         aCTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGa                                                                                                              <  2:841687/78‑1 (MQ=255)

                                                                         aCTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGa                                                                                                              >  1:841687/1‑78 (MQ=255)

                                                                         aCTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGAc                                                 <  2:578845/139‑1 (MQ=255)

                                                                              ccTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAAtct                                            >  2:698589/1‑139 (MQ=255)

                                                                              ccTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAAtct                                            >  1:709931/1‑139 (MQ=255)

                                                                               ctctTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTccc                                                                                      <  1:62282/96‑1 (MQ=255)

                                                                               ctctTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTccc                                                                                      >  2:62282/1‑96 (MQ=255)

                                                                                     ccGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGcc                                     >  1:58096/1‑139 (MQ=255)

                                                                                       ggTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGa                                   >  2:471876/1‑139 (MQ=255)

                                                                                        gTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGAt                                  >  2:347072/1‑139 (MQ=255)

                                                                                           cccTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGc                               <  2:193650/139‑1 (MQ=255)

                                                                                           cccTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGc                               <  1:471876/139‑1 (MQ=255)

                                                                                               aTGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTg                                                                                   <  2:754519/83‑1 (MQ=255)

                                                                                               aTGCCGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTg                                                                                   >  1:754519/1‑83 (MQ=255)

                                                                                                   cGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATa                       >  2:173479/1‑139 (MQ=255)

                                                                                                   cGGGTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATa                       <  1:347072/139‑1 (MQ=255)

                                                                                                     ggTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATc                                 <  2:48682/127‑1 (MQ=255)

                                                                                                     ggTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATc                                 >  1:48682/1‑127 (MQ=255)

                                                                                                          tttttATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATACTCtgtg                <  2:58096/139‑1 (MQ=255)

                                                                                                          tttttATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATACTCtggg                >  2:244227/1‑137 (MQ=255)

                                                                                                               aTGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACCATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTAATACTCTGTGGGCGt           <  2:503089/139‑1 (MQ=255)

                                                                                                                tGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATACTCTGTGGGCGTc          >  2:366374/1‑139 (MQ=255)

                                                                                                                    tGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATc                                 >  2:256203/1‑112 (MQ=255)

                                                                                                                    tGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATc                                 <  1:256203/112‑1 (MQ=255)

                                                                                                                     gAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGa                         >  2:177923/1‑119 (MQ=255)

                                                                                                                     gAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGa                         <  1:177923/119‑1 (MQ=255)

                                                                                                                      aGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTccc                                                                                      >  2:521500/1‑57 (MQ=255)

                                                                                                                      aGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTccc                                                                                      <  1:521500/57‑1 (MQ=255)

                                                                                                                        tAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATACTCTGTGGGCGTCATCCCata  <  2:414708/139‑1 (MQ=255)

AACTTACTGAGAGCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTATGTCTGAGTAAAACTCTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATACTCTGTGGGCGTCATCCCATA  >  NC_000913/3664859‑3665117

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A