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
A8 F1 I1 R1	771	44.8	2153074	94.1%	2026042	109.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,019,150	C→T	E302K (GAA→AAA)	ompA ←	outer membrane protein A (3a,II*,G,d)

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,019,150	0	C	T	87.0%	103.5 / 9.0	46	E302K (GAA→AAA)	ompA	outer membrane protein A (3a,II*,G,d)
Reads supporting (aligned to +/- strand): ref base C (3/3); new base T (19/21); total (22/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.01e-01

CGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGTCACAGGTGTTGCCAGTAACCGGGTTGGATTCGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGGAGATCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACC  >  NC_000913/1019022‑1019279

cGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTAAGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGTCACAGGTGTTGCCAGTAACCGGGTTGGATTTGCCCATACCa                                                                                                                         >  2:762000/1‑139 (MQ=255)

 ggCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGTCACAGGTGTTGCCAGTAACCGGGTTGGATTTGCCCATACCAc                                                                                                                        <  1:762000/139‑1 (MQ=255)

      aGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGTTTCGCGTTGTCACAGGTGTTGCCAGTAACCGGGTTGGATTTGCCCATACCACGTGCg                                                                                                                   <  2:628016/139‑1 (MQ=255)

                  tttGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGTCACAGGTGTTGCCAGTAACCGGGTTGGATTTGCCCATACCACGTGCGGAGATCTTGTCt                                                                                                       >  1:222353/1‑139 (MQ=255)

                          cTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGTCACAGGTGTTGCCAGTAACCGGGTTGGATTTGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGa                                                                                                <  2:522233/138‑1 (MQ=255)

                          cTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGTCACAGGTGTTGCCAGTAACCGGGTTGGATTTGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGa                                                                                                >  1:522233/1‑138 (MQ=255)

                          cTTTAACTTCGATATCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGTCTCAGGTGTTGCCAGTAACCGGGTTGGATTCGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGAt                                                                                               >  2:713758/1‑139 (MQ=255)

                            ttAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGTCACAGGTGTTGCCAGTAACCGGGTTGGATTTGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATAc                                                                                             >  2:973249/1‑139 (MQ=255)

                                   cGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGTCACAGGTGTTGCCAGTAACCGGGTTGGATTTGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATAc                                                                                             >  1:62084/1‑132 (MQ=255)

                                   cGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGTCACAGGTGTTGCCAGTAACCGGGTTGGATTTGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATAc                                                                                             <  2:62084/132‑1 (MQ=255)

                                    gATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGTCACAGGTGTTGCCAGTAACCGGGTTGGATTTGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGga                                                                                      >  1:1027606/1‑138 (MQ=255)

                                    gATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGTCACAGGTGTTGCCAGTAACCGGGTTGGATTTGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGga                                                                                      <  2:1027606/138‑1 (MQ=255)

                                       ctctACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGTCACAGGTGTTGCCAGTAACCGGGTTGGATTTGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGGAGATc                                                                                  <  2:871619/139‑1 (MQ=255)

                                          tACGCGACGATCCGGAGCCATGCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGTCACAGGTGTTGCCAGTAACCGGGTTGGATTTTCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGGAGATCAgg                                                                               <  1:796057/139‑1 (MQ=255)

                                              cgacgaTCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGTCACAGGTGTTGCCAGTAACCGGGTTGGATTTGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGGAGATCAGGTAAt                                                                           <  1:973249/139‑1 (MQ=255)

                                                 cgaTCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGTCACAGGTGTTGCCAGTAACCGGGTTGGATTCGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGGAGATCAGGTAATcaa                                                                        >  2:968579/1‑139 (MQ=255)

                                                          gCCAGGCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGTCACAGGTGTTGCCAGTAACCGGGTTGGATTCGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGGAGATCAGGTAATCAACAACAGACt                                                               <  1:713758/139‑1 (MQ=255)

                                                              ggCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGTCACAGGTGTTGCCAGTAACCGGGTTGGATTTGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGGAGATCAGGTAATca                                                                         >  2:929076/1‑125 (MQ=255)

                                                              ggCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGTCACAGGTGTTGCCAGTAACCGGGTTGGATTTGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGGAGATCAGGTAATca                                                                         <  1:929076/125‑1 (MQ=255)

                                                               gCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGTCACAGGTGTTGCCAGTAACCGGGTTGGATTTGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGGAGATCAGGTAATCAACAACAGACTGAGCa                                                          >  2:480591/1‑139 (MQ=255)

                                                                                 aCGCTGTTTCACGTTGTCACAGGTGTTGCCAGTAACCGGGTTGGATTTGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTgg                                                                                       >  1:55808/1‑92 (MQ=255)

                                                                                 aCGCTGTTTCACGTTGTCACAGGTGTTGCCAGTAACCGGGTTGGATTTGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTgg                                                                                       <  2:55808/92‑1 (MQ=255)

                                                                                     tGTTTCACGTTGTCACAGGTGTTGCCAGTAACCGGGTTGGATTTGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGAAGATCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGt                                    >  2:716043/1‑139 (MQ=255)

                                                                                     tGTTTCACGTTGTCACAGCTGTTGCCAGTAACCGGGTTGGATTCGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGGAGATCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGt                                    >  2:596567/1‑139 (MQ=255)

                                                                                         tCACGTTGTCACAGGTGTTGCCAGTAACCGGGTTGGATTTGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGGAGATCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTa                                <  1:844962/139‑1 (MQ=255)

                                                                                              ttGTCACAGGTGTTGCCAGTAACCGGGTTGGATTCGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGGAGATCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGt                           <  1:968579/139‑1 (MQ=255)

                                                                                                 tCACAGGTGTTGCCAGTAACCGGGTTGGATTTGCCCATACCACGTg                                                                                                                     >  2:1074510/1‑46 (MQ=255)

                                                                                                 tCACAGGTGTTGCCAGTAACCGGGTTGGATTTGCCCATACCACGTg                                                                                                                     <  1:1074510/46‑1 (MQ=255)

                                                                                                 tCACAGGTGTTGCCAGTAACCGGGTTGGATTTGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGGAGATCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTa                                >  1:324678/1‑131 (MQ=255)

                                                                                                 tCACAGGTGTTGCCAGTAACCGGGTTGGATTTGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGGAGATCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTa                                <  2:324678/131‑1 (MQ=255)

                                                                                                           tGCCAGTAACCGGGTTGGATTTGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGGAGATCAGGTAATCAACAACAGACTGAGCa                                                          <  2:790459/95‑1 (MQ=255)

                                                                                                           tGCCAGTAACCGGGTTGGATTTGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGGAGATCAGGTAATCAACAACAGACTGAGCa                                                          >  1:790459/1‑95 (MQ=255)

                                                                                                           tGCCAGTAACCGGGTTGGATTTGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGGAGATCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGcg              >  1:499263/1‑139 (MQ=255)

                                                                                                           tGCCAGTAACCGGGTTGGATTTGCACATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGGAGATCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGAt                 >  2:728948/1‑136 (MQ=255)

                                                                                                           tGCCAGTAACCGGATTGGATTTGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGGAGATCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGATTGTAAGCGTCAGAACCGAt                 <  1:728948/136‑1 (MQ=255)

                                                                                                            gCCAGTAACCGGGTTGGATTTGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGGAGATCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGcgg             >  1:367097/1‑139 (MQ=255)

                                                                                                            gCCAGTAACCGGGTTGGATTTGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGGAGATCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGcgg             >  2:452660/1‑139 (MQ=255)

                                                                                                             ccAGTAACCGGGTTGGATTTGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGGAGATCAgg                                                                               <  2:478921/72‑1 (MQ=255)

                                                                                                             ccAGTAACCGGGTTGGATTTGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGGAGATCAgg                                                                               >  1:478921/1‑72 (MQ=255)

                                                                                                             ccAGTAACCGGGTTGGATTTGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGGAGATCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGcggt            <  2:739171/139‑1 (MQ=255)

                                                                                                             ccAGTAACCGGGTTGGATTTGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGGAGATCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGcggt            <  1:452660/139‑1 (MQ=255)

                                                                                                             ccAGTAACCGGGTTGGATTTGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGGAGATCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGcggt            <  2:499263/139‑1 (MQ=255)

                                                                                                             ccAGTAACCGGGTTGGATTCGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGGAGATCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGcggt            <  1:596567/139‑1 (MQ=255)

                                                                                                                   aCCGGGTTGGATTTGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGGAGATCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGa                                               >  1:925519/1‑98 (MQ=255)

                                                                                                                   aCCGGGTTGGATTTGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGGAGATCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGa                                               <  2:925519/98‑1 (MQ=255)

                                                                                                                       ggTTGGATTTGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGGAGATCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAAcc  <  2:222353/139‑1 (MQ=255)

CGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCAGCACGCTGTTTCACGTTGTCACAGGTGTTGCCAGTAACCGGGTTGGATTCGCCCATACCACGTGCGGAGATCTTGTCTGCCGGGATACCTTTGGAGATCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACC  >  NC_000913/1019022‑1019279

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