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 F17 I0 R1	43	55.2	1410130	81.3%	1146435	215.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,424,240	G→T	32.9%	L153F (TTG→TTT)	trkG →	Rac prophage; potassium transporter subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,424,240	0	G	T	32.9%	31.9 / 3.6	23	L153F (TTG→TTT)	trkG	Rac prophage; potassium transporter subunit
Reads supporting (aligned to +/- strand): ref base G (4/11); new base T (6/2); total (10/13)
Fisher's exact test for biased strand distribution p-value = 3.93e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTTTGGATTTTGTTTTCTGTTATTAGTGCATTCCCTTTATGGATTGACTCAGAACTTAATTTAACGTTCATTGATGCTCTGTTTGAAGGGGTTTCTGGAATAACAACAACAGGAGCAACTGTAATTGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGGTTGCTGTA‑TTGCCA‑TTATTGGGTATTGGTGGTGCAAAGCTTTATCAGTCAGAAATGCCGGGGCCATTTAAGGATGACAAACTCACTCCCCGCCTGGCCGATACGTCACGGACACTGTGGATAACTTATTCTTTATTAGGTATTGCTTGTATTGTCTGTTATAGACTTGCAGGAATGCCTTTGTTTGATGCTATTTGTCACGGGATTTCCACAGTTTCGCTTGGTGGTTTCTCAACT  >  NC_000913/1424016‑1424465

ttttGGATTTTGTTTTCTGTTATTAGTGCATTCCCTTTATGGATTGACTCAGAACTTAATTTAACGTTCATTGATGCTCTGTTTGAAGGGGTTTCTGGAATAACAACAACAGGAGCAACTGTAATTGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGGTTGCTGTA‑TTGCCa                                                                                                                                                                                                                                 <  1:106819/228‑1 (MQ=255)

          tGTTTTCTGTTATTAGTGCATTCCCTTTATGGATTGACTCAGAACTTAATTTAACGTTCATTGATGCTCTGTTTGAAGGGGTTTCTGGAATAACAACAACAGGAGCAACTGTAATTGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGGTTTTTGTT‑TTTCTATTTATTggga                                                                                                                                                                                                                       >  2:582224/1‑227 (MQ=255)

                             aTTCCCTTTATGGATTGACTCAGAACTTAATTTAACGTTCATTGATGCTCTGTTTGAAGGGGTTTCTGGAATAACACCAACAGGAGCAACTGTAATTGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGCGTTATTGTTCTGGCGGTTGGTGTA‑TTGCCA‑TTATTGGGGGTTGGTGGTGCTAAGCtttt                                                                                                                                                                                                   >  1:100503/1‑227 (MQ=255)

                               tCCCTTTATGGATTGACTCAGAACTTAATTTAACGTTCATTGATGCTCTGTTTGAAGGGGTTTCTGGAATAACAACAACAGGAGCAACTGTAATTGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGGTTGCTGTA‑TTTGCC‑TTTTTGGGGTTTGTTGGTGCTAAGtttttt                                                                                                                                                                                                  >  1:236322/1‑225 (MQ=255)

                               tCCCTTTATGGATTGACTCAGAACTTAATTTAACGTTCATTGATGCTCTGTTTGAAGGGGTTTCTGGAATAACAACAACAGGAGCAACTGTAATTGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCGGGCGGTTGC‑GTATTTGTAT‑TTATTGTGGATTTGGGGTGCAAAGCgttctt                                                                                                                                                                                                 >  1:97745/1‑225 (MQ=255)

                                    ttATGGATTGACTCAGAACTTAATTTAACGTTCATTGATGCTCTGTTTGAAGGGGTTTCTGGAATAACAACAACAGGAGCAACTGTAATTGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGGTGGTTGTA‑TTGCCC‑TTATTTGGGATTGTTGGGTCGAAGCTTTTtcagtct                                                                                                                                                                                            >  1:632212/1‑227 (MQ=255)

                                               cctaggaCTTAATTTAACGTTCATTGATTCTCTGTTTGAAGGGGTTTCTGGAATAACAACAACAGGAGCAACTGTAATTGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGGTTGCTGTA‑TTGCCA‑TTATTGGGTATTGGTGGTGCAAAGCTTTATCAGTCAGAAATGCCggg                                                                                                                                                                                 <  1:582224/222‑1 (MQ=255)

                                                       ttAATTTAACGTTCATTGATGCTCTGTTTGAAGGGGTTTCTGGAATAACAACAACAGGAGCAACTGTAATTGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGGTTGCTGTA‑TTGCCA‑TTATTGGGTATTGGTGGTGCAAAGCTTTATCAGTCAGAAATGCCGGGGCCATTTa                                                                                                                                                                         <  1:447593/228‑1 (MQ=255)

                                                                cGTTCATTGATGCTCTGTTTGAAGGGGTTTCTGGAATAACAACAACAGGAGCAACTGTAATTGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGGTTTCTGTA‑TTTTAC‑TTTTTTGGTATTGGTGGTGCAATGCTGTTTTATTCTGAAAAGACCGGGGCGTTTAAGGATGAc                                                                                                                                                                 >  2:38577/1‑227 (MQ=255)

                                                                    cATTGATGCTCTGTTTGAAGGGGTTTCTGGAATAACAACAACAGGAGCAACTGTAATTGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGGTTGCTGTA‑TTTTCA‑TTATTGGGGGATGGTTGGTCAAAGCTTTATTAGTCCGGAATGCCGGGGCCATTTAATGATGACAAac                                                                                                                                                             >  1:319631/1‑227 (MQ=255)

                                                                        tattttttttttGAAGGGGTTTCTGGAAAAACAACAACAGGAGCAACTTTAATTGATGAGGTTAGTTTATTGCCTGGGGCATGTTTGTTTTTTCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCGGGCGGTTGATGTA‑TTGCCA‑TTATTGGGTATTGGTGGTGCAAAGCTTTATCAGTCAGAAATGCCGGGGCCATTTAAGGATGACAAactcact                                                                                                                                                        <  2:100503/219‑1 (MQ=255)

                                                                                           tttCTGGAATAACAACAACAGGAGCAACTGTAATTGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGGTTGCTGTA‑TTTcc                                                                                                                                                                                                                                  >  2:208118/1‑136 (MQ=255)

                                                                                            ttCTGGAATAACAACAACAGGAGCAACTGTAATTGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGGTTGCTGTA‑TTGCCa                                                                                                                                                                                                                                 <  1:208118/136‑1 (MQ=255)

                                                                                                                     aCTGTAATTGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGGTTGCTGTA‑TTGCCA‑TTATTGGGTATTGGTGGTGCAAAGCTTTATCAGTCAGAAATGCCGGGGCCATTTAAGGATGACAAACTCACTCCCCGCCTGGCCGATACGTCACGGACACTGTGGATAACTTATTCt                                                                                                           <  1:38577/228‑1 (MQ=255)

                                                                                                                         ttaTTGATGTTTTTATTTTATTTCCTGGGGCATTTTTTTATTTTCGGTCAAAGTTAAATTTTATAGGTGGTTTAGGATTTATTGTTCTGGGGGTTGCTGTA‑TTGCCA‑TTATTGGGTATTGGTGGTGCAAAGCTTTATCAGTCAGAAATGCCGGGGCCATTTAAGGATGACAAACTCACTCCCCGCCTGGCCGATACGTCACGGACACTGTGGATAACTTATTCTttat                                                                                                       <  2:38644/226‑1 (MQ=255)

                                                                                                                            ttGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGGTTGCTGTA‑TTGCCA‑TTATTGGGTATTGGTGGTGCAAAGCTTTATCAGTCAGAAATGCCGGGGCCATTTAAGGATGACAAACTCACTCCCCGCCTGGCCGATACGTCACGGACACTGTGGATAACTTATTCTttatt                                                                                                      <  1:484830/226‑1 (MQ=255)

                                                                                                                                 gatgTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGGTTGCTGTA‑TTGCCA‑TTATTGGGTATTGGTGGTGCAAAGCTTTATCAGTCAGAAATGCCGGGGCCATTTAAGGATGACAAACTCACTCCCCGCCTGGCCGATACGTCACGGACACTGTGGATAACTTATTCTttatta                                                                                                     <  1:95131/222‑1 (MQ=255)

                                                                                                                                            aTTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGGTTGCTGTA‑TTGCCA‑TTATTGGGTATTGGTGGTGCAAAGCTTTATCAGTCAGAAATGCCGGGGCCATTTAAGGATGACAAACTCACTCCCCGCCTGGCCGATACGTCACGGACACTGTGGATAACTTATTCTTTATTAGGTATTGCTTGTATTGt                                                                                    <  1:94947/228‑1 (MQ=255)

                                                                                                                                                               tACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGGTTGCTGTA‑TTTCCA‑TTATTGGGTATTGGTGGTGCAAAGCTTTATCCGTCAGAAATGCCGGGGCCATTTTAGGATGACAAACTCACTCCCCGCCTGGCCGATACGTCACGGGAACTTTGGATAAATTATTTTTTATTAGGGATTGCTTTGAATGGCTGTTATAGACttttcgga                                                                 >  1:153648/1‑222 (MQ=255)

                                                                                                                                                                    tCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGGTTGCTGTA‑TTGCCA‑TTATTGGGTATTGGTGGTGCAAAGGTTTATTAGTTAGAAATGCCGGGGCCATTTAAGGATGGCAAACTCACTCCCCCCCTGGCCGCTACGCCACGGACACTGTGGGGAACTTATTCTTTATTTTGTGTTGGTTGTATTGTCTGTTATTTACTTTCAGGGATgtc                                                            >  2:494607/1‑226 (MQ=255)

                                                                                                                                                                                          ggttgtTTTGGTGTTTTTTTTCTTGCTGTTGCTGTA‑TTTCCA‑TTATTGGGTATTGGTGGTGCAAAGCTTTATCAGTCAGAAATGCCGGGGCCATTTAAGGATGACAAATCTACTCCCCGCCTGGCCGATACGTCACGGACACTGTGGATAACTTATTCTTTATTAGGTATTGCTTGTATTGTCTGTTATAGACTTGCAGGAATGCCTTTGTTTGATGCTATTTGTCAc                                      <  2:153648/228‑1 (MQ=255)

                                                                                                                                                                                                                          tttA‑TTTCCA‑TTATTGGGTTTTGGTGGTGCAAAGCTTTATCAGTCAGAAAGGCCGGGGCAATTTAAGGATGAAAAACTCACTCCCCGCCTGGCCGATACGTCACGGACACTGTGGATAACTTATTCTTTATTAGGTATTGCTTGTATTGTCTGTTATAGACTTGCAGGAATGCCTTTGTTTGATGCTATTTGTCACGGGATTTCCACAGTTTCGCTTGGTGGTTtctc      <  2:537546/226‑1 (MQ=255)

                                                                                                                                                                                                                                tGCCA‑TTATTGGGTTTTGGGGGTGCAAAGCTGTATCAGTCAGAAATGCCGGGGCCATTTAAGGATGACAAACTCACTCCCCGCCTGGCCGATACGTCACGTACACTGTGGATAACTTATTCTTTATTAGGTATTGCTTGTATTGTCTGTTATAGACTTGCAGGAATGCCTTTGTTTGATGCTATTTGTCACGGGATTTCCACAGTTTCGCTTGGTGGTTTCTCAACt  <  1:467018/227‑1 (MQ=255)

TTTTGGATTTTGTTTTCTGTTATTAGTGCATTCCCTTTATGGATTGACTCAGAACTTAATTTAACGTTCATTGATGCTCTGTTTGAAGGGGTTTCTGGAATAACAACAACAGGAGCAACTGTAATTGATGATGTTAGTTCATTACCTCGGGCATATTTGTACTATCGGTCACAGTTAAATTTTATAGGTGGTTTAGGAGTTATTGTTCTGGCGGTTGCTGTA‑TTGCCA‑TTATTGGGTATTGGTGGTGCAAAGCTTTATCAGTCAGAAATGCCGGGGCCATTTAAGGATGACAAACTCACTCCCCGCCTGGCCGATACGTCACGGACACTGTGGATAACTTATTCTTTATTAGGTATTGCTTGTATTGTCTGTTATAGACTTGCAGGAATGCCTTTGTTTGATGCTATTTGTCACGGGATTTCCACAGTTTCGCTTGGTGGTTTCTCAACT  >  NC_000913/1424016‑1424465

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A