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
A20 F60 I1 R1	17	35.9	1226658	98.8%	1211938	139.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,393,241	T→G	V5V (GTT→GTG)	mppA →	murein tripeptide ABC transporter periplasmic binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,393,241	0	T	G	96.7%	109.0 / ‑3.7	30	V5V (GTT→GTG)	mppA	murein tripeptide ABC transporter periplasmic binding protein
Reads supporting (aligned to +/- strand): ref base T (0/1); new base G (11/18); total (11/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

TATATTGATACTTAAAACATTTGATGCTTCCTTTGTCACTTTTTTGATGGAAGTTGTTTGCATTTCTTTAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTCAGCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCTGGATC  >  NC_000913/1393105‑1393374

tatatTGATACTTAAAACATTTGATGCTTCCTTTGTCACTTTTTTGATGGAAGTTGTTTGCATTTCTTTAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTGTCa                                                                                                                                    <  1:105238/140‑1 (MQ=255)

tatatTGATACTTAAAACATTTGATGCTTCCTTTGTCACTTTTTTGATGGAAGTTGTTTGCATTTCTTTAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTGTCa                                                                                                                                    <  1:584715/140‑1 (MQ=255)

    ttGATACTTAAAACATTTGATGCTTCCTTTGTCACTTTTTTGATGGAAGTTGTTTGCATTTCTTTAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTgtcagtca                                                                                                                                >  2:277085/1‑140 (MQ=255)

    ttGATACTTAAAACATTTGATGCTTCCTTTGTCACTTTTTTGATGGAAGTTGTTTGCATTTCTTTAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTgtcagtca                                                                                                                                >  1:320043/1‑140 (MQ=255)

     tGATACTTAAAACATTTGATGCTTCCTTTGTCACTTTTTTGATGGAAGTTGTTTGCATTTCTTTAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTGTCAGTCAc                                                                                                                               <  1:78019/140‑1 (MQ=255)

       aTACTTAAAACATTTGATGCTTCCTTTGTCACTTTTTTGATGGAAGTTGTTTGCATTTCTTTAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTGTCAGTCACgt                                                                                                                             <  2:539526/140‑1 (MQ=255)

       aTACTTAAAACATTTGATGCTTCCTTTGTCACTTTTTTGATGGAAGTTGTTTGCATTTCTTTAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTGTCAGTCACgt                                                                                                                             >  1:419578/1‑140 (MQ=255)

        tACTTAAAACATTTGATGCTTCCTTTGTCACTTTTTTGATGGAAGTTGTTTGCATTTCTTTAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTGTCAGTCACgtg                                                                                                                            <  2:518467/140‑1 (MQ=255)

         aCTTAAAACATTTGATGCTTCCTTTGTCACTTTTTTGATGGAAGTTGTTTGCATTTCTTTAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTGTCAGTCACgtgt                                                                                                                           >  1:114056/1‑140 (MQ=255)

         aCTTAAAACATTTGATGCTTCCTTTGTCACTTTTTTGATGGAAGTTGTTTGCATTTCTTTAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTGTCAGTCACgtgt                                                                                                                           >  1:265971/1‑140 (MQ=255)

                aCATTTGATGCTTCCTTTGTCACTTTTTTGATGGAAGTTGTTTGCATTTCTTTAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTGTCAGTCACGTGTTGTgcgc                                                                                                                    <  1:124250/140‑1 (MQ=255)

                          cTTCCTTTGTCACTTTTTTGATGGAAGTTGTTTGCATTTCTTTAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTGTCAGTCACGTGTTGTGCGCTGTTGGTcag                                                                                                          <  1:277085/140‑1 (MQ=255)

                                         ttttGATGGAAGTTGTTTGCATTTCTTTAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTGTCAGTCACGTGTTGTGCGCTGTTGGTCAGCAGCATTTCTCTTTc                                                                                           >  1:569511/1‑140 (MQ=255)

                                               tGGAAGTTGTTTGCATTTCTTTAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTGTCAGTCACGTGTTGTGCGCTGTTGGTCAGCAGCATTTCTCTTTCGTAtgc                                                                                     <  2:265971/140‑1 (MQ=255)

                                                             aTTTCTTTAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTGTCAGTCACGTGTTGTGCGCTGTTGGTCAGCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGa                                                                       >  2:244312/1‑140 (MQ=255)

                                                              tttCTTTAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTGTCAGTCACGTGTTGTGCGCTGTTGGTCAGCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAg                                                                      <  2:235216/140‑1 (MQ=255)

                                                                  tttAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTGTCAGTCACGTGTTGTGCGCTGTTGGTCAGCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGc                                                                  <  1:385799/140‑1 (MQ=255)

                                                                    tAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTGTCAGTCACGTGTTGTGCGCTGTTGGTCAGCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGa                                                                       >  1:100095/1‑133 (MQ=255)

                                                                    tAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTGTCAGTCACGTGTTGTGCGCTGTTGGTCAGCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGa                                                                       <  2:100095/133‑1 (MQ=255)

                                                                           aaaCAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTGTCAGTCACGTGTTGTGCGCTGTTGGTCAGCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGcaca                                                               <  1:136905/134‑1 (MQ=255)

                                                                           aaaCAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTGTCAGTCACGTGTTGTGCGCTGTTGGTCAGCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGcaca                                                               >  2:136905/1‑134 (MQ=255)

                                                                           aaaCAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTGTCAGTCACGTGTTGTGCGCTGTTGGTCAGCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTg                                                         >  1:212331/1‑140 (MQ=255)

                                                                             aCAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTGTCAGTCACGTGTTGTGCGCTGTTGGTCAGCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGc                                                       <  2:419578/140‑1 (MQ=255)

                                                                                          cATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTGTCAGTCACGTGTTGTGCGCTGTTGGTCAGCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAg                                          <  2:55323/140‑1 (MQ=255)

                                                                                                ttttAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTGTCAGTCACGTGTTGTGCGCTGTTGGTCAGCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTg                                    <  1:355456/140‑1 (MQ=255)

                                                                                                   tAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTCAGCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTgcgc                                 <  1:240806/140‑1 (MQ=255)

                                                                                                   tAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTGTCAGTCACGTGTTGTGCGCTGTTGGTCAGCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTgcgc                                 <  2:212331/140‑1 (MQ=255)

                                                                                                           gTTAGAGGGAAACTTATGAAGCACTCTGTGTCAGTCACGTGTTGTGCGCTGTTGGTCAGCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTaa                         >  1:575205/1‑140 (MQ=255)

                                                                                                                      aCTTATGAAGCACTCTGTGTCAGTCACGTGTTGTGCGCTGTTGGTCAGCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTg              <  1:440268/140‑1 (MQ=255)

                                                                                                                                cACTCTGTGTCAGTCACGTGTTGTGCGCTGTTGGTCAGCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCTGGa    <  2:457981/140‑1 (MQ=255)

                                                                                                                                  ctctGTGTCAGTCACGTGTTGTGCGCTGTTGGTCAGCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCTGGATc  >  1:258519/1‑140 (MQ=255)

                                                                                                                                  ctctGTGTCAGTCACGTGTTGTGCGCTGTTGGTCAGCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCTGGATc  >  1:561013/1‑140 (MQ=255)

TATATTGATACTTAAAACATTTGATGCTTCCTTTGTCACTTTTTTGATGGAAGTTGTTTGCATTTCTTTAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTCAGCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCTGGATC  >  NC_000913/1393105‑1393374

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `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