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
A7 F50 I2 R1	209	44.2	1360995	98.7%	1343302	150.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	667,534	T→C	E228E (GAA→GAG)	mrdA ←	penicillin‑binding protein 2, transpeptidase involved in peptidoglycan synthesis

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	667,534	0	T	C	100.0%	158.3 / NA	42	E228E (GAA→GAG)	mrdA	penicillin‑binding protein 2, transpeptidase involved in peptidoglycan synthesis
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (21/21); total (21/21)

TCGGTGACTACCACAGCTGCGCGGCTACCCGCCAGCAGCGTTTCAATATATTGCTGGAGTTTGAGATCCAGCGTCAGGTAAATATCGTGTCCGGCTTGCGGTGGTACTTCTTTTAACTGGCGAATAACACGCCCACGGTTGTTAACTTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCATAGTAACGCTCAATGCCCAGCTTACCGATATCATGCGTTGCCGCATAGTTGGCCAGTTTGCCGTCATTATTCAGGCGTTCGACGTCTTTATCGTTGATTTT  >  NC_000913/667388‑667677

tCGGTGACTACCACAGCTGCGCGGCTACCCGCCAGCAGCGTTTCAATATATTGCTGGAGTTTGAGATCCAGCGTCAGGTAAATATCGTGTCCGGCTTGCGGTGGTACTTCTTTTAACTGGCGAATAACACGCCCACGGTTGTTAACCTc                                                                                                                                               <  1:377848/149‑1 (MQ=255)

tCGGTGACTACCACAGCTGCGCGGCTACCCGCCAGCAGCGTTTCAATATATTGCTGGAGTTTGAGATCCAGCGTCAGGTAAATATCGTGTCCGGCTTGCGGTGGTACTTCTTTTAACTGGCGAATAACACGCCCACGGTTGTTAACCTCa                                                                                                                                              >  1:484599/1‑150 (MQ=255)

          ccACAGCTGCGCGGCTCCCCGCCAGCAGCGTTTCAATATATTGCTGGAGTTTGAGATCCAGCGTCAGGTAAATATCGTGTCCGGCTTGCGGTGGTACTTCTTTTAACTGGCGAATAACACGCCCACGGTTGTTAACCTCAACCTCTTc                                                                                                                                      <  2:237989/148‑1 (MQ=255)

                  gcgcGGCTCCCCGCCAGCAGCGTTTCAATATATTGCTGGAGTTTGAGATCCAGCGTCAGGTAAATATCGTGTCCGGCTTGCGGTGGTACTTCTTTTAACTGGCGAATAACACGCCCACGGTTGTTAACCTCAACCTCTTCATAACCGGTc                                                                                                                            <  2:586752/150‑1 (MQ=255)

                  gcgcGGCTACCCGCCAGCAGCGTTTCAATATATTGCTGGAGTTTGAGATCCAGCGTCAGGTAAATATCGTGTCCGGCTTGCGGTGGTACTTCTTTTAACTGGCGAATAACACGCCCACGGTTGTTAACCTCAACCTCTTCATAACCGGTCt                                                                                                                           >  2:332155/1‑151 (MQ=255)

                      ggCTACCCGCCAGCAGCGTTTCAATATATTGCTGGAGTTTGAGATCCAGCGTCAGGTAAATATCGTGTCCGGCTTGCGGTGGTACTTCTTTTAACTGGCGAATAACACGCCCACGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGAc                                                                                                                        <  1:445923/150‑1 (MQ=255)

                             cGCCAGCAGCGTTTCAATATATTGCTGGAGTTTGAGATCCAGCGTCAGGTAAATATCGTGTCCGGCTTGCGGTGGTACTTCTTTTAACTGGCGAATAACACGCCCACGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGACCGTgcagc                                                                                                                >  1:438373/1‑151 (MQ=255)

                                       gTTTCAATATATTGCTGGAGTTTGAGATCCAGCGTCAGGTAAATATCGTGTCCGGCTTGCGGTGGTACTTCTTTTAACTGGCGAATAACACGCCCACGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCAt                                                                                                      >  1:577435/1‑151 (MQ=255)

                                           cAATATATTGCTGGAGTTTGAGATCCAGCGTCAGGTAAATATCGTGTCCGGCTTGCGGTGGTACTTCTTTTAACTGGCGAATAACACGCCCACGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCATAGt                                                                                                   >  1:27316/1‑150 (MQ=255)

                                           cAATATATTGCTGGAGTTTGAGAGCCAGCGTCAGGTAAATATCGTGTCCGGCTTGCGGTGGTACTTCTCTTAACTGTCGAATAACACGCCCACGGTTGTTAACCTCAACCTTTTCATAACCGGTCTGACCGTGCAGCACCTCTTCATCGt                                                                                                   <  2:234091/150‑1 (MQ=255)

                                                  ttGCTGGAGTTTGAGATCCAGCGTCAGGTAAATATCGTGTCCGGCTTGCGGTGGTACTTCTTTTAACTGGCGAATAACACGCCCACGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCATAGTAACGCTc                                                                                            >  1:436629/1‑150 (MQ=255)

                                                   tGCTGGAGTTTGAGATCCAGCGTCAGGTAAATATCGTGTCCGGCTTGCGGTGGTACTTCTTTTAACTGGCGAATAACACGCCCACGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCATAGTAACGCTCa                                                                                           <  1:517846/150‑1 (MQ=255)

                                                        gAGTTTGAGATCCAGCGTCAGGTAAATATCGTGTCCGGCTTGCGGTGGTACTTCTTTTAACTGGCGAATAACACGCCCACGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCATAGTAACGCTCAATGccc                                                                                     >  2:446766/1‑151 (MQ=255)

                                                         aGTTTGAGATCCAGCGTCAGGTAAATATCGTGTCCGGCTTGCGGTGGTACTTCTTTTAACTGGCGAATAACACGCCCACGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCATAGTAACGCTCAATGCCCa                                                                                    <  2:232751/151‑1 (MQ=255)

                                                                   ccAGCGTCAGGTAAATATCGTGTCCGGCTTGCGGTGGTACTTCTTTTAACTGGCGAATAACACGCCCACGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCATAGTAACGCTCAATGCCCAGCTTACCGa                                                                           <  1:1892/150‑1 (MQ=255)

                                                                         tCAGGTAAATATCGTGTCCGGCTTGCGGTGGTACTTCTTTTAACTGGCGAATAACACGCCCACGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCATAGTAACGCTCAATGCCCAGCTTACCGATATCATg                                                                    >  2:422325/1‑151 (MQ=255)

                                                                             gTAAATATCGTGTCCGGCTTGCGGTGGTACTTCTTTTAACTGGCGAATAACGCGCCCACGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCATAGTAACGCTCAATGCCCAGCTTACCGATATCATGCGtt                                                                <  2:278991/151‑1 (MQ=255)

                                                                               aaaTATCGTGTCCGGCTTGCGGTGGTACTTCTTTTAACTGGCGAATAACACGCCCACGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCATAGTAACGCTCAATGCCCAGCTTACCGATATCATGCGTTGc                                                              >  1:201986/1‑151 (MQ=255)

                                                                               aaaTATCGTGTCCGGCTTGCGGTGGTACTTCTTTTAACTGGCGAATAACACGCCCACGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCATAGTAACGCTCAATGCCCAGCTTACCGATATCATGCGTTGc                                                              >  1:576239/1‑151 (MQ=255)

                                                                                     cGTGTCCGGCTTGCGGTGGTACTTCTTTTAACTGGCGAATAACACGCCCACGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCATAGTAACGCTCAATGCCCAGCTTACCGATATCATGCGTTGCCGCAt                                                         <  2:273713/150‑1 (MQ=255)

                                                                                      gtgtCCGGCTTGCGGTGGTACTTCTTTTAACTGGCGAATAACACGCCCACGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCATAGTAACGCTCAATGCCCAGCTTACCGATATCATGCGTTGCCGCATAg                                                       <  2:264837/151‑1 (MQ=255)

                                                                                      gtgtCCGGCTTGCGGTGGTACTTCTTTTAACTGGCGAATAACACGCCCACGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCATAGTAACGCTCAATGCCCAGCTTACCGATATCATGCGTTGCCGCATAg                                                       <  2:27316/151‑1 (MQ=255)

                                                                                           cGGCTTGCGGTGGTACTTCTTTTAACTGGCGAATAACACGCCCACGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCATAGTAACGCTCAATGCCCAGCTTACCGATATCATGCGTTGCCGCATAGTTGGc                                                  <  1:605284/151‑1 (MQ=255)

                                                                                               ttGCGGTGGTACTTCTTTTAACTGGCGAATAACACGCCCACGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCATAGTAACGCTCAATGCCCAGCTTACCGATATCATGCGTTGCCGCATAGTTGGCCAGt                                              >  2:4301/1‑151 (MQ=255)

                                                                                                 gCGGTGGTACTTCTTTTAACTGGCGAATAACACGCCCACGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCATAGTAACGCTCAATGCCCAGCTTACCGATATCATGCGTTGCCGCATAGTTGGCCAGttt                                            <  2:196604/151‑1 (MQ=255)

                                                                                                     tggtACTTCTTTTAACTGGCGAATAACACGCGCACGGTTGTTAACCTCAACCTCTTCATATCCGGTCTGTCCGTGCAGCTCATCCTCATAGTATCGCTCAATGCCCAGCTTACCGATATCATGCGTTGCCTCATAGTTGGCCAgg                                              <  2:597034/145‑2 (MQ=255)

                                                                                                      ggtACTTCTTTTAACTGGCGAATAACACGCCCACGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCATAGTAACGCTCAATGGCCAGCTTACCGATATCATGCGTTGCCGCATAGTTGGCCAGTTTGCCGt                                       <  2:438646/151‑1 (MQ=255)

                                                                                                      ggtACTTCTTTTAACTGGCGAATAACACGCCCACGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCATAGTAACGCTCAATGCCCAGCTTACCGATATCATGCGTTGCCGCATAGTTGGCCAGTTTGCCGt                                       >  1:303066/1‑151 (MQ=255)

                                                                                                      ggtACTTCTTTTAACTGGCGAATAACACGCCCACGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCATAGTAACGCTCAATGCCCAGCTTACCGATATCATGCGTTGCCGCATAGTTGGCCAGTTTGCCGt                                       >  2:468314/1‑151 (MQ=255)

                                                                                                          cttcttTTAACTGGCGAATAACACGCCCACGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCATAGTAACGCTCAATGCCCAGCTTACCGATATCATGCGTTGCCGCATAGTTGGCCAGTTTGCCGTCatt                                   >  1:561524/1‑151 (MQ=255)

                                                                                                              ttttAACTGGCGAATAACACGCCCACGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCATAGTAACGCTCAATGCCCAGCTTACCGATATCATGCGTTGCCGCATAGTTTGCCAGTTTGCCGTCATTATTc                               >  1:34240/1‑151 (MQ=255)

                                                                                                               tttAACTGGCGAATAACACGCCCACGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCATAGTAACGCTCAATGCCCAGCTTACCGATATCATGCGTTGCCGCATAGTTGGCCAGTTTGCCGTCattatt                                <  2:452523/149‑1 (MQ=255)

                                                                                                                     tGGCGAATAACACGCCCACGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCATAGTAACGCTCAATGCCCAGCTTACCGATATCATGCGTTGCCGCATAGTTGGCCAGTTTGCCGTCATTATTCAGGCGtt                        >  1:446254/1‑151 (MQ=255)

                                                                                                                      ggCGAATAACACGCCCACGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCATAGTAACGCTCAATGCCCAGCTTACCGATATCATGCGTTGCCGCATAGTTGGCCAGTTTGCCGTCATTATTCAGGCGTTc                       >  1:532186/1‑151 (MQ=255)

                                                                                                                         gAATAACACGCCCGCGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGACCGGGCAGCACATCTTCATAGTAACGCTCAATGCCCAGCTTACCGATATCATGCGTTGCCGCATAGTTTGCCAGTTTGCCGTCATTATTCAGGCGTTCGAc                    <  2:471893/151‑1 (MQ=255)

                                                                                                                         gAATAACACGCCCACGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCATAGTAACGCTCAATGCCCAGCTTACCGATATCATGCGTTGCCGCATAGTTGGCCAGTTTGCCGTCATTATTCAGGCGTTCGAc                    >  1:434642/1‑151 (MQ=255)

                                                                                                                                acGCCCACGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCATAGTAACGCTCAATGCCCAGCTTACCGATATCATGCGTTGCCGCATAGTTGGCCAGTTTGCCGTCATTATTCAGGCGTTCGACGTCttt              >  1:363005/1‑150 (MQ=255)

                                                                                                                                acGCCCACGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCATAGTAACGCTCAATGCCCAGCTTACCGATATCATGCGTTGCCGCATAGTTGGCCAGTTTGCCGTCATTATTCAGGCGTTCGACGTCTTTa             <  2:29156/151‑1 (MQ=255)

                                                                                                                                 cGCCCACGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCATAGTAACGCTCAATGCCCAGCTTACCGATATCATGCGTTGCCGCATAGTTGGCCAGTTTGCCGTCATTATTCAGGCGTTCGACGTCTTTAt            >  2:82914/1‑151 (MQ=255)

                                                                                                                                  gCCAACGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCATAGTAACGCTCAATGCCCAGCTTACCGATATCATGCGTTGCCGCATAGTTGGCCCGTTTGCCGTCATTATTCAGGCGTTCGACGTCTTTa             >  2:515204/1‑149 (MQ=255)

                                                                                                                                       cGGTTGTTAACCTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCATAGTAACGCTCAATGCCCAGCTTACCGATATCATGCGTTGCCGCATAGTTGGCCAGTTTGCCGTCATTATTCAGGCGTTCGACGTCTTTATCGTTg       <  2:350431/150‑1 (MQ=255)

                                                                                                                                            gttAACCTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCATAGTAACGCTCAATGCCCAGCTTACCGATATCATGCGTTGCCGCATAGTTGGCCAGTTTGCCGTCATTATTCAGGCGTTCGACGTCTTTATCGTTGAtttt  <  1:528854/150‑1 (MQ=255)

TCGGTGACTACCACAGCTGCGCGGCTACCCGCCAGCAGCGTTTCAATATATTGCTGGAGTTTGAGATCCAGCGTCAGGTAAATATCGTGTCCGGCTTGCGGTGGTACTTCTTTTAACTGGCGAATAACACGCCCACGGTTGTTAACTTCAACCTCTTCATAACCGGTCTGACCGTGCAGCACATCTTCATAGTAACGCTCAATGCCCAGCTTACCGATATCATGCGTTGCCGCATAGTTGGCCAGTTTGCCGTCATTATTCAGGCGTTCGACGTCTTTATCGTTGATTTT  >  NC_000913/667388‑667677

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A