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
A12 F28 I1 R1	123	51.0	1731148	99.3%	1719029	138.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,565,289	G→A	S431S (AGC→AGT)	glgP ←	glycogen phosphorylase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,565,289	0	G	A	100.0%	143.0 / NA	43	S431S (AGC→AGT)	glgP	glycogen phosphorylase
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (20/23); total (20/23)

AGCCAGCGACGCGGCGTCACACCGTTGGTGACGTTGGTGAAACGACCCGGGAAGATTTTCGCAAAGTCGGCAAACAACGATTGCACCATCAGATTAGAGTGCAGTTCCGATACACCGTTAACTTTGTGGCTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGATTCATCAATGATCGACGCCCGTCCCAGCAGATCGGTATCGTTCGGATACTGTTCCTGCAAGGTTTTCAGGAAATAGTCGTT  >  NC_000913/3565161‑3565417

agccagcGACGCGGCGTCACACCGTTGGTGACGTTGGTGAAACGACCCGGGAAGATTTTCGCAAAGTCGGCAAACAACGATTGCACCATCAGATTAGAGTGCAGTTCCGATACACCGTTAACTTTGTGACTCACaacaac                                                                                                                       >  2:364912/1‑140 (MQ=255)

      cGACGCGGCGTCACACCGTTGGTGACGTTGGTGAAACGACCCGGGAAGATTTTCGCAAAGTCGGCAAACAACGATTGCACCATCAGATTAGAGTGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCgccag                                                                                                                 >  2:225194/1‑140 (MQ=255)

       gACGCGGCGTCACACCGTTGGTGACGTTGGTGAAACGACCCGGGAAGATTTTCGCAAAGTCGGCAAACAACGATTGCACCATCAGATTAGAGTGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCgccagc                                                                                                                <  1:814690/140‑1 (MQ=255)

              cgTCACACCGTTGGTGACGTTGGTGAAACGACCCGGGAAGATTTTCGCAAAGTCGGCAAACAACGATTGCACCATCAGATTAGAGTGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCa                                                                                                         <  1:749142/140‑1 (MQ=255)

                   cacCGTTGGTGACGTTGGTGAAACGACCCGGGAAGATTTTCGCAAAGTCGGCAAACAACGATTGCACCATCAGATTAGAGTGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGc                                                                                                    >  2:29557/1‑140 (MQ=255)

                      cgttggtgacgttggtgaAACGACCCGGGAAGATTTTCGCAAAGTCGGCAAACAACGATTGCACCATCAGATTAGAGTGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGcaca                                                                                                 >  2:300553/1‑140 (MQ=255)

                              acgttggtgaAACGACCCGGGAAGATTTTCGCAAAGTCGGCAAACAACGATTGCACCATCAGATTAGAGTGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGAcc                                                                                         >  1:579651/1‑140 (MQ=255)

                               cgttggtgaAACGCCCCGGGAAGATTTTCGCAAAGTCGGCAAACAACGATTGCACCATCAGATTAGAGTGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCg                                                                                        <  2:51866/140‑1 (MQ=255)

                               cgttggtgaAACGACCCGGGAAGATTTTCGCAAAGTCGGCAAACAACGATTGCACCATCAGATTAGAGTGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCg                                                                                        <  2:338313/140‑1 (MQ=255)

                                   ggtgaAACGACCCGGGAAGATTTTCGCAAAGTCGGCAAACAACGATTGCACCATCAGATTAGAGTGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTgg                                                                                    >  2:703870/1‑140 (MQ=255)

                                    gtgaAACGACCCGGGAAGATTTTCGCAAAGTCGGCAAACAACGATTGCACCATCAGATTAGAGTGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGa                                                                                   <  1:300553/140‑1 (MQ=255)

                                    gtgaAACGACCCGGGAAGATTTTCGCAAAGTCGGCAAACAACGATTGCACCATCAGATTAGAGTGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGa                                                                                   <  1:604220/140‑1 (MQ=255)

                                      gaAACGACCCGGGAAGATTTTCGCAAAGTCGGCAAACAACGATTGCACCATCAGATTAGAGTGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGAtt                                                                                 <  1:264522/140‑1 (MQ=255)

                                          cGACCCGGGAAGATTTTCGCAAAGTCGGCAAACAACGATTGCACCATCAGATTAGAGTGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGATtcatc                                                                             >  2:321909/1‑140 (MQ=255)

                                            aCCCGGGAAGATTTTCGCAAAGTCGGCAAACAACGATTGCACCATCAGATTAGAGTGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGATTCATCaa                                                                           <  1:364912/140‑1 (MQ=255)

                                            aCCCGGGAAGATTTTCGCAAAGTCGGCAAACAACGATTGCACCATCAGATTAGAGTGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGATTCATCaa                                                                           >  1:90378/1‑140 (MQ=255)

                                                     gATTTTCGCAAAGTCGGCAAACAACGATTGCACCATCAGATTAGAGTGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGATTCATCAATGATCGACg                                                                  <  1:29557/140‑1 (MQ=255)

                                                       ttttCGCAAAGTCGGCAAACAACGATTGCACCATCAGATTAGAGTGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGATTCATCAATGATCGACGcc                                                                <  2:365438/140‑1 (MQ=255)

                                                       ttttCGCAAAGTCGGCAAACAACGATTGCACCATCAGATTAGAGTGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGATTCATCAATGATCGACGcc                                                                <  1:225194/140‑1 (MQ=255)

                                                        tttCGCAAAGTCGGCAAACAACGATTGCACCATCAGATTAGAGTGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGATTCATCAATGATCGACGccc                                                               >  1:403419/1‑140 (MQ=255)

                                                           cGCAAAGTCGGCAAACAACGATTGCACCATCAGATTAGAGTGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGATTCATCAATGATCGACGCCCGTc                                                            >  2:811708/1‑140 (MQ=255)

                                                               aaGTCGGCAAACAACGATTGCACCATCAGATTAGAGTGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGATTCATCAATGATCGACGCCCGTCCcag                                                        <  1:811708/140‑1 (MQ=255)

                                                               aaGTCGGCAAACAACGATTGCACCATCAGATTAGAGTGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGATTCATCAATGATCGACGCCCGTCCcag                                                        <  2:150478/140‑1 (MQ=255)

                                                               aaGTCGGCAAACAACGATTGCACCATCAGATTAGAGTGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGATTCATCAATGATCGACGCCCGTCCcag                                                        <  2:403419/140‑1 (MQ=255)

                                                                aGTCGGCAAACAACGATTGCACCATCAGATTAGAGTGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGATTCATCAATGATCGACGCCCGTCCcagc                                                       >  1:563043/1‑140 (MQ=255)

                                                                    ggCAAACAACGATTGCACCATCAGATTAGAGTGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGATTCATCAATGATCGACGCCCGTCCCAGCAGAt                                                   <  1:502696/140‑1 (MQ=255)

                                                                          caacGATTGCACCATCAGATTAGAGTGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGATTCATCAATGATCGACGCCCGTCCCAGCAGATCGGTAt                                             <  1:703870/140‑1 (MQ=255)

                                                                          caacGATTGCACCATCAGATTAGAGTGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGATTCATCAATGATCGACGCCCGTCCCAGCAGATCGGTAt                                             <  2:763616/140‑1 (MQ=255)

                                                                            acGATTGCACCATCAGATTAGAGTGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGATTCATCAATGATCGACGCCCGTCCCAGCAGATCGGTATCg                                           >  1:308756/1‑140 (MQ=255)

                                                                                   cACCATCAGATTAGAGTGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGATTCATCAATGATCGACGCCCGTCCCAGCAGATCGGTATCGTTCGGAt                                    <  2:579651/140‑1 (MQ=255)

                                                                                               agagTGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGATTCATCAATGATCGACGCCCGTCCCAGCAGATCGGTATCGTTCGGATACTGTTCCTGCa                        <  2:563043/140‑1 (MQ=255)

                                                                                               agagTGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGATTCATCAATGATCGACGCCCGTCCCAGCAGATCGGTATCGTTCGGATACTGTTCCTGCa                        <  2:90378/140‑1 (MQ=255)

                                                                                                 agTGCAGTTCCGATACACCGTTAACTTTGTGACTCACGACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGATTCATCAATGATCGACGCCCGTCCCAGCAGATCGGTATCGTTCGGATACTGTTCCTGCAAg                      >  2:27279/1‑140 (MQ=255)

                                                                                                 agTGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGATTCATCAATGATCGACGCCCGTCCCAGCAGATCGGTATCGTTCGGATACTGTTCCTGCAAg                      >  1:204080/1‑140 (MQ=255)

                                                                                                   tGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGATTCATCAATGATCGACGCCCGTCCCAGCAGATCGGTATCGTTCGGATACTGTTCCTGCa                        >  1:798976/1‑136 (MQ=255)

                                                                                                   tGCAGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGATTCATCAATGATCGACGCCCGTCCCAGCAGATCGGTATCGTTCGGATACTGTTCCTGCa                        <  2:798976/136‑1 (MQ=255)

                                                                                                      aGTTCCGATACACCGTTAACTTTGTGACTCACGACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGATTCATCAATGATCGACGCCCGTCCCAGCAGATCGGTATCGTTCGGATACTGTTCCTGCAAGGtttt                 <  1:27279/140‑1 (MQ=255)

                                                                                                      aGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGATTCATCAATGATCGACGCCCGTCCCAGCAGATCGGTATCGTTCGGATACTGTTCCTGCaa                       <  2:186894/134‑1 (MQ=255)

                                                                                                      aGTTCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGATTCATCAATGATCGACGCCCGTCCCAGCAGATCGGTATCGTTCGGATACTGTTCCTGCaa                       >  1:186894/1‑134 (MQ=255)

                                                                                                        ttCCGATACACCGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGATTCATCAATGATCGACGCCCGTCCCAGCAGATCGGTATCGTTCGGATACTGTTCCTGCAAGGTTTTCa               >  1:848523/1‑140 (MQ=255)

                                                                                                                  ccGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGATTCATCAATGATCGACGCCCGTCCCAGCAGATCGGTATCGTTCGGATACTGTTCCTGCAAGGTTTTCAGGAAATAGTc     >  2:649500/1‑140 (MQ=255)

                                                                                                                   cGTTAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGATTCATCAATGATCGACGCCCGTCCCAGCAGATCGGTATCGTTCGGATACTGTTCCTGCAAGGTTTTCAGGAAATAGTCg    >  1:658294/1‑140 (MQ=255)

                                                                                                                     ttAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGATTCATCAATGATCGACGCCCGTCCCAGCAGATCGGTATCGTTCGGATACTGTTCCTGCAAGGTTTTCAGGAAATAGTCGtt  <  2:308756/140‑1 (MQ=255)

                                                                                                                     ttAACTTTGTGACTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGATTCATCAATGATCGACGCCCGTCCCAGCAGATCGGTATCGTTCGGATACTGTTCCTGCAAGGTTTTCAGGAAATAGTCGtt  >  1:608022/1‑140 (MQ=255)

AGCCAGCGACGCGGCGTCACACCGTTGGTGACGTTGGTGAAACGACCCGGGAAGATTTTCGCAAAGTCGGCAAACAACGATTGCACCATCAGATTAGAGTGCAGTTCCGATACACCGTTAACTTTGTGGCTCACAACAACCGCCAGCCAGGCCATACGCACACGACGACCGTTGGATTCATCAATGATCGACGCCCGTCCCAGCAGATCGGTATCGTTCGGATACTGTTCCTGCAAGGTTTTCAGGAAATAGTCGTT  >  NC_000913/3565161‑3565417

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A