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
A1 F28 I1 R1	163	52.9	1786516	99.3%	1774010	139.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,576,342	C→T	pseudogene (2208/2721 nt)	yjiV →	putative uncharacterized protein YjiV

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,576,342	0	C	T	97.8%	155.3 / ‑4.1	46	pseudogene (2208/2721 nt)	yjiV	putative uncharacterized protein YjiV
Reads supporting (aligned to +/- strand): ref base C (0/1); new base T (25/20); total (25/21)
Fisher's exact test for biased strand distribution p-value = 4.57e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.47e-01

CAACGCTGTCGAGCGGGTCAAAGACATTCAGATCCACAAACAGTTGAATGGACCACTGTCGCAGTTTGGGCAACGCTTCTGGGACGTGCTGTTTAACGACCATGAAGAAGCGCAGTCACTGATGAATAACACGCGAATTACCGGCGTTCACTATACCGATCGCTATCTGCAAAACCCGGTTGCGCTGGCGTTGTTGGGATCAATTCTGAGACCGCTAAAAACAAAGCTGACCGATGGCGCTGAAGTGACGCTGGATACGCTATTTA  >  NC_000913/4576213‑4576478

caACGCTGTCGAGCGGGTCAAAGACATTCAGATCCACAAACAGTTGAATGGACCACTGTCGCAGTTTGGGCAACGCTTCTGGGACGTGCTGTTTAACGACCATGAAGAAGCGCAGTCACTGATGAATAATACGCGAATTa                                                                                                                                >  2:7986/1‑140 (MQ=255)

 aaCGCTGTCGAGCGGGTCAAAGACATTCAGATCCACAAACAGTTGAATGGACCACTGTCGCAGTTTGGGCAACGCTTCTGGGACGTGCTGTTTAACGACCATGAAGAAGCGCAGTCACTGATGAATAATACGCGAATTAc                                                                                                                               <  2:262940/140‑1 (MQ=255)

     cTGTCGAGCGGGTCAAAGACATTCAGATCCACAAACAGTTGAATGGACCACTGTCGCAGTTTGGGCAACGCTTCTGGGACGTGCTGTTTAACGACCATGAAGAAGCGCAGTCACTGATGAATAATACGCGAATTACCGGc                                                                                                                           <  2:270963/140‑1 (MQ=255)

     cTGTCGAGCGGGTCAAAGACATTCAGATCCACAAACAGTTGAATGGACCACTGTCGCAGTTTGGGCAACGCTTCTGGGACGTGCTGTTTAACGACCATGAAGAAGCGCAGTCACTGATGAATAATACGCGAATTACCGGc                                                                                                                           <  1:848438/140‑1 (MQ=255)

     cTGTCGAGCGGGTCAAAGACATTCAGATCCACAAACAGTTGAATGGACCACTGTCGCAGTTTGGGCAACGCTTCTGGGACGTGCTGTTTAACGACCATGAAGAAGCGCAGTCACTGATGAATAATACGCGAATTACCGGc                                                                                                                           <  1:6249/140‑1 (MQ=255)

     cTGTCGAGCGGGTCAAAGACATTCAGATCCACAAACAGTTGAATGGACCACTGTCGCAGTTTGGGCAACGCTTCTGGGACGTGCTGTTTAACGACCATGAAGAAGCGCAGTCACTGATGAATAACACGCGAATTACCGGc                                                                                                                           <  1:143013/140‑1 (MQ=255)

        tCGAGCGGGTCAAAGACATTCAGATCCACAAACAGTTGAATGGACCACTGTCGCAGTTTGGGCAACGCTTCTGGGACGTGCTGTTTAACGACCATGAAGAAGCGCAGTCACTGATGAATAATACGCGAATTACCGGCGtt                                                                                                                        >  2:332765/1‑140 (MQ=255)

        tCGAGCGGGTCAAAGACATTCAGATCCACAAACAGTTGAATGGACCACTGTCGCAGTTTGGGCAACGCTTCTGGGACGTGCTGTTTAACGACCATGAAGAAGCGCAGTCACTGATGAATAATACGCGAATTACCGGCGtt                                                                                                                        <  1:756791/140‑1 (MQ=255)

                gTCAAAGACATTCAGATCCACAAACAGTTGAATGGACCACTGTCGCAGTTTGGGCAACGCTTCTGGGACGTGCTGTTTAACGACCATGAAGAAGCGCAGTCACTGATGAATAATACGCGAATTACCGGCGTTCACTATAc                                                                                                                >  1:245467/1‑140 (MQ=255)

                     aGACATTCAGATCCACAAACAGTTGAATGGACCACTGTCGCAGTTTGGGCAACGCTTCTGGGACGTGCTGTTTAACGACCATGAAGAAGCGCAGTCACTGATGAATAATACGCGAATTACCGGCg                                                                                                                          >  2:618888/1‑125 (MQ=255)

                     aGACATTCAGATCCACAAACAGTTGAATGGACCACTGTCGCAGTTTGGGCAACGCTTCTGGGACGTGCTGTTTAACGACCATGAAGAAGCGCAGTCACTGATGAATAATACGCGAATTACCGGCg                                                                                                                          <  1:618888/125‑1 (MQ=255)

                          ttCAGATCCACAAACAGTTGAATGGACCACTGTCGCAGTTTGGGCAACGCTTCTGGGACGTGCTGTTTAACGACCATGAAGAAGCGCAGTCACTGATGAATAATACGCGAATTACCGGCGTTCACTATACCGATCGCTAt                                                                                                      >  1:269979/1‑140 (MQ=255)

                           tCAGATCCACAAACAGTTGAATGGACCACTGTCGCAGTTTGGGCAACGCTTCTGGGACGTGCTGTTTAACGACCATGAAGAAGCGCAGTCACTGATGAATAATACGCGAATTACCGGCGTTCACTATACCGATCGCTATc                                                                                                     >  2:199583/1‑140 (MQ=255)

                               aTCCACAAACAGTTGAATGGACCACTGTCGCAGTTTGGGCAACGCTTCTGGGACGTGCTGTTTAACGACCATGAAGAAGCGCAGTCACTGATGAATAATACGCGAATTACCGGCGTTCACTATAc                                                                                                                <  1:625691/125‑1 (MQ=255)

                               aTCCACAAACAGTTGAATGGACCACTGTCGCAGTTTGGGCAACGCTTCTGGGACGTGCTGTTTAACGACCATGAAGAAGCGCAGTCACTGATGAATAATACGCGAATTACCGGCGTTCACTATAc                                                                                                                >  2:625691/1‑125 (MQ=255)

                                           ttGAATGGACCACTGTCGCAGTTTGGGCAACGCTTCTGGGACGTGCTGTTTAACGACCATGAAGAAGCGCAGTCACTGATGAATAATACGCGAATTACCGGCGTTCACTATACCGATCGCTATCTGCAAAACCCGGTTgc                                                                                     >  1:739386/1‑140 (MQ=255)

                                             gAATGGACCACTGTCGCAGTTTGGGCAACGCTTCTGGGACGTGCTGTTTAACGACCATGAAGAAGCGCAGTCACTGATGAATAATACGCGAATTACCGGCGTTCACTATACCGATCGCTATCTGCAAAACCCGGTTgcgc                                                                                   <  1:89197/140‑1 (MQ=255)

                                                  gACCACTGTCGCAGTTTGGGCAACGCTTCTGGGACGTGCTGTTTAACGACCATGAAGAAGCGCAGTCACTGATGAATAATACGCGAATTACCGGCGTTCACTATACCGATCGCTATCTGCAAAACCCGGTTGCGCTGGCg                                                                              <  2:269979/140‑1 (MQ=255)

                                                       cTGTCGCAGTTTGGGCAACGCTTCTGGGACGTGCTGTTTAACGACCATGAAGAAGCGCAGTCACTGATGAATAATACGCGAATTACCGGCGTTCACTATACCGATCGCTATCTGCAAAACCCGGTTGCGCTGGCgttgtt                                                                         <  2:739386/140‑1 (MQ=255)

                                                        tGTCGCAGTTTGGGCAACGCTTCTGGGACGTGCTGTTTAACGACCATGAAGAAGCGCAGTCACTGATGAATAATACGCGAATTACCGGCGTTCACTATACCGATCGCTATCTGCAAAACCCGGTTGCGCTGGCGttgttg                                                                        >  1:667324/1‑140 (MQ=255)

                                                           cGCAGTTTGGGCAACGCTTCTGGGACGTGCTGTTTAACGACCATGAAGAAGCGCAGTCACTGATGAATAATACGCGAATTACCGGCGTTCACTATACCGATCGCTATCTGCAAAACCCGGTTGCGCTGGCGTTGTTGGGa                                                                     <  1:199583/140‑1 (MQ=255)

                                                             cAGTTTGGGCAACGCTTCTGGGACGTGCTGTTTAACGACCATGAAGAAGCGCAGTCACTGATGAATAATACGCGAATTACCGGCGTTCACTATACCGATCGCTATCTGCAAAACCCGGTTGCGCTGGCGTTGTTGGGATc                                                                   <  2:667324/140‑1 (MQ=255)

                                                                    ggCAACGCTTCTGGGACGTGCTGTTTAACGACCATGAAGAAGCGCAGTCACTGATGAATAATACGCGAATTACCGGCGTTCACTATACCGATCGCTATCTGCAAAACCCGGTTGCGCTGGCGTTGTTGGGATCAATTCTg                                                            >  1:273256/1‑140 (MQ=255)

                                                                                      tGCTGTTTAACGACCATGAAGAAGCGCAGTCACTGATGAATAATACGCGAATTACCGGCGTTCACTATACCGATCGCTATCTGCAAAACCCGGTTGCGCTGGCGTTGTTGGGATCAATTCTGAGACCGCt                                                    <  1:426637/130‑1 (MQ=255)

                                                                                      tGCTGTTTAACGACCATGAAGAAGCGCAGTCACTGATGAATAATACGCGAATTACCGGCGTTCACTATACCGATCGCTATCTGCAAAACCCGGTTGCGCTGGCGTTGTTGGGATCAATTCTGAGACCGCt                                                    >  2:426637/1‑130 (MQ=255)

                                                                                      tGCTGTTTAACGACCATGAAGAAGCGCAGTCACTGATGAATAATACGCGAATTACCGGCGTTCACTATACCGATCGCTATCTGCAAAACCCGGTTGCGCTGGCGTTGTTGGGATCAATTCTGAGACCGCTAAAAACAAAg                                          >  2:761298/1‑140 (MQ=255)

                                                                                      tGCTGTTTAACGACCATGAAGAAGCGCAGTCACTGATGAATAATACGCGAATTACCGGCGTTCACTATACCGATCGCTATCTGCAAAACCCGGTTGCGCTGGCGTTGTTGGGATCAATTCTGAGACCGCTAAAAACAAAg                                          >  1:257074/1‑140 (MQ=255)

                                                                                      tGCTGTTTAACGACCATGAAGAAGCGCAGTCACTGATGAATAATACGCGAATTACCGGCGTTCACTATACCGATCGCTATCTGCAAAACCCGGTTGCGCTGGCGTTGTTGGGATCAATTCTGAGACCGCTAAAAACAAAg                                          >  2:782214/1‑140 (MQ=255)

                                                                                      tGCTGTTTAACGACCATGAAGAAGCGCAGTCACTGATGAATAATACGCGAATTACCGGCGTTCACTATACCGATCGCTATCTGCAAAACCCGGTTGCGCTGGCGTTGTTGGGATCAATTCTGAGACCGCTAAAAACAAAg                                          >  2:50712/1‑140 (MQ=255)

                                                                                      tGCTGTTTAACGACCATGAAGAAGCGCAGTCACTGATGAATAATACGCGAATTACCGGCGTTCACTATACCGATCGCTATCTGCAAAACCCGGTTGCGCTGGCGTTGTTGGGATCAATTCTGAGACCGCTAAAAACAAAg                                          >  2:93563/1‑140 (MQ=255)

                                                                                        cTGTTTAACGACCATGAAGAAGCGCAGTCACTGATGAATAATACGCGAATTACCGGCGTTCACTATACCGATCGCTATCTGCAAAACCCGGTTGCGCTGGCGTTGTTGGGATCAATTCTGAGACCGCTAAAAACAAAGCt                                        >  1:707712/1‑140 (MQ=255)

                                                                                                   ccATGAAGAAGCGCAGTCACTGATGAATAATACGCGAATTACCGGCGTTCACTATACCGATCGCTATCTGCAAAACCCGGTTGCGCTGGCGTTGTTGGGATCAATTCTGAGACCGCTAAAAACAAAGCTGACCGATGgcg                             >  1:308612/1‑140 (MQ=255)

                                                                                                     aTGAAGAAGCGCAGTCACTGATGAATAATACGCGAATTACCGGCGTTCACTATACCGATCGCTATCTGCAAAACCCGGTTGCGCTGGCGTTGTTGGGATCAATTCTGAGACCGCTAAAAACAAAGCTGACCGATGGCGCt                           <  2:273256/140‑1 (MQ=255)

                                                                                                     aTGAAGAAGCGCAGTCACTGATGAATAATACGCGAATTACCGGCGTTCACTATACCGATCGCTATCTGCAAAACCCGGTTGCGCTGGCGTTGTTGGGATCAATTCTGAGACCGCTAAAAACAAAGCTGACCGATGGCGCt                           >  1:424508/1‑140 (MQ=255)

                                                                                                             gcgcAGTCACTGATGAATAATACGCGAATTACCGGCGTTCACTATACCGATCGCTATCTGCAAAACCCGGTTGCGCTGGCGTTGTTGGGATCAATTCTGAGACCGCTAAAAACAAAGCTGACCGATGGCGCTGAAGTGAc                   <  2:707712/140‑1 (MQ=255)

                                                                                                             gcgcAGTCACTGATGAATAATACGCGAATTACCGGCGTTCACTATACCGATCGCTATCTGCAAAACCCGGTTGCGCTGGCGTTGTTGGGATCAATTCTGAGACCGCTAAAAACAAAGCTGACCGATGGCGCTGAAGTGAc                   >  1:648631/1‑140 (MQ=255)

                                                                                                              cgcAGTCACTGATGAATAATACGCGAATTACCGGCGTTCACTATACCGATCGCTATCTGCAAAACCCGGTTGCGCTGGCGTTGTTGGGATCAATTCTGAGACCGCTAAAAACAAAGCTGACCGATGGCGCTGAAGTGACg                  >  2:537423/1‑140 (MQ=255)

                                                                                                              cgcAGTCACTGATGAATAATACGCGAATTACCGGCGTTCACTATACCGATCGCTATCTGCAAAACCCGGTTGCGCTGGCGTTGTTGGGATCAATTCTGAGACCGCTAAAAACAAAGCTGACCGATGGCGCTGAAGTGACg                  >  2:224873/1‑140 (MQ=255)

                                                                                                              cgcAGTCACTGATGAATAATACGCGAATTACCGGCGTTCACTATACCGATCGCTATCTGCAAAACCCGGTTGCGCTGGCGTTGTTGGGATCAATTCTGAGACCGCTAAAAACAAAGCTGACCGATGGCGCTGAAGTGACg                  >  2:65862/1‑140 (MQ=255)

                                                                                                              cgcAGTCACTGATGAATAATACGCGAATTACCGGCGTTCACTATACCGATCGCTATCTGCAAAACCCGGTTGCGCTGGCGTTGTTGGGATCAATTCTGAGACCGCTAAAAACAAAGCTGACCGATGGCGCTGAAGTGACg                  <  1:129652/140‑1 (MQ=255)

                                                                                                              cgcAGTCACTGATGAATAATACGCGAATTACCGGCGTTCACTATACCGATCGCTATCTGCAAAACCCGGTTGCGCTGGCGTTGTTGGGATCAATTCTGAGACCGCTAAAAACAAAGCTGACCCATGGCGCTGAAGTGACg                  >  2:57125/1‑140 (MQ=255)

                                                                                                                     aCTGATGAATAATACGCGAATTACCGGCGTTCACTATACCGATCGCTATCTGCAAAACCCGGTTGCGCTGGCGTTGTTGGGATCAATTCTGAGACCGCTAAAAACAAAGCTGACCGATGGCGCTGAAGTGACGCTGGATa           <  2:438222/140‑1 (MQ=255)

                                                                                                                       tgatgaATAATACGCGAATTACCGGCGTTCACTATACCGATCGCTATCTGCAAAACCCGGTTGCGCTGGCGTTGTTGGGATCAATTCTGAGACCGCTAAAAACAAAGCTGACCGATGGCGCTGAAGTGACGCTGGATACg         >  2:611107/1‑140 (MQ=255)

                                                                                                                       tgatgaATAATACGCGAATTACCGGCGTTCACTATACCGATCGCTATCTGCAAAACCCGGTTGCGCTGGCGTTGTTGGGATCAATTCTGAGACCGCTAAAAACAAAGCTGACCGATGGCGCTGAAGTGACGCTGGATACg         <  1:50712/140‑1 (MQ=255)

                                                                                                                       tgatgaATAATACGCGAATTACCGGCGTTCACTATACCGATCGCTATCTGCAAAACCCGGTTGCGCTGGCGTTGTTGGGATCAATTCTGAGACCGCTAAAAACAAAGCTGACCGATGGCGCTGAAGTGACGCTGGATACg         <  1:65862/140‑1 (MQ=255)

                                                                                                                              tAATACGCGAATTACCGGCGTTCACTATACCGATCGCTATCTGCAAAACCCGGTTGCGCTGGCGTTGTTGGGATCAATTCTGAGACCGCTAAAAACAAAGCTGACCGATGGCGCTGAAGTGACGCTGGATACGCTATTta  <  1:635155/140‑1 (MQ=255)

CAACGCTGTCGAGCGGGTCAAAGACATTCAGATCCACAAACAGTTGAATGGACCACTGTCGCAGTTTGGGCAACGCTTCTGGGACGTGCTGTTTAACGACCATGAAGAAGCGCAGTCACTGATGAATAACACGCGAATTACCGGCGTTCACTATACCGATCGCTATCTGCAAAACCCGGTTGCGCTGGCGTTGTTGGGATCAATTCTGAGACCGCTAAAAACAAAGCTGACCGATGGCGCTGAAGTGACGCTGGATACGCTATTTA  >  NC_000913/4576213‑4576478

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A