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
A11 F20 I0 R1	35	38.1	1546666	86.7%	1340959	142.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,111,164	G→T	32.1%	R101L (CGT→CTT)	opgH →	osmoregulated periplasmic glucans (OPGs) biosynthesis protein H

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,111,164	0	G	T	32.1%	38.3 / 13.2	33	R101L (CGT→CTT)	opgH	osmoregulated periplasmic glucans (OPGs) biosynthesis protein H
Reads supporting (aligned to +/- strand): ref base G (9/13); new base T (6/5); total (15/18)
Fisher's exact test for biased strand distribution p-value = 4.88e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAACAAGCCTGGCCAGATTCACTTGCTGATGGACAGTTAATTAAAGACGACGAAGGGCGCGATCAGCTGAAGGCGATGCCAGAAGCAAAACGCTCCTCGATGTTTCCCGACCCGTGGCGTACCAACCCGGTAGGCCGTTTCTGGGATCGCCTGCGTGGACGCGATGTCACGCCGCGCTATCTGGCTCGTTTGACCAAAGAAGAGCAGGAGAGCGAGCAAAAGTGGCGTACCGTCGGTACCATCCGCCGTTACATTCTGTTGATCCTGACGCTCGCGCA  >  NC_000913/1111028‑1111305

gAACAAGCCTGGCCAGATTCACTTGCTGATGGACAGTTAATTAAAGACGACGAAGGGCGGGAGCGGCTGAAGGCGCTGCCAGAAGCAAAACGCTCCTCGATGTTTCCCGACCCGTGGCGTACCAACCCGGTAGGCCTTTTCTg                                                                                                                                         >  1:318473/1‑143 (MQ=255)

 aaCAAGCCTGGTCAGATTCATTTTCTTATGTATAGTTAATTAAAGACGACGAAGGGCGCGAGCAGCGGAAGGCGATGCCAGAAGCAAAACGCTCCTCGATGTTTCCCGACCCGTGGCGTACCAACCCGGTAGGCCGTTTCTgg                                                                                                                                        <  1:706538/143‑1 (MQ=255)

          ggtcggATTCACCGGCTGATGGACAGTTAATTAAAGACGACGAAGTGCGCGATCAGCTGAAGGCGATGCCAGAAGCAAAACGCTCCTCGATGTTTCCCGACCCGTGGCGTACCAACCCGGTAGGCCGTTTCTGGGATCGCCTg                                                                                                                               <  2:389641/138‑1 (MQ=255)

             cAGATTCACTTGCTGATGGACAGTTAATTAAAGACGACGAAGGGCGCGATCAGCTGAAGGCGATGACAGAAGCAAAACGCTCCTCGATGTTTCCCGACCGGTGGCGGACCAACCCGGTAGGGCGGTGCTGAGATCGGCtctgc                                                                                                                            >  1:636639/1‑139 (MQ=255)

               gATTCACTTGCTGATGGACAGTTAATTAAAGACGACGAAGGGCGCGATCAGCTGAAGGCGATGCCAGAAGCAAAACGCTCCTCGATGTTTCCCGACCCGTGGCGTACCAACCCGGTAGGCCTTTTCTGGGATCGCCTGCGTgg                                                                                                                          >  2:583212/1‑143 (MQ=255)

                aTTCACTTGCTGATGGACAGTTAATTATATACGACGTAGGGCGCGATCAGCTGAAGGCGATGCCAGAAGCAAAACGCTCCTCGAGGTTTCCCGACCCGTGGCGTACCAACCCGGTAGGCCGTTTCTGGGATCGCCTGCGTGGa                                                                                                                         <  1:211587/143‑1 (MQ=255)

                           gATGGACAGTTAATTAAAGACGACGAAGGGCGCGATCAGCTGAAGGCGATGCCAGAAGCAAAACGCTCCTCGATGTTTCCCGACCCGTGGCGTACCAACCCGGTAGGCCGTTTCTAGGATCGCCTGCGTGGACACGATGTCAc                                                                                                              >  1:116458/1‑143 (MQ=255)

                             tGGACAGTTAATTAAAGACGACGAAGGGCGTGATCAGCTGAAGGCGATGCCAGAAGCAAAACGCTCCTCGATGTTTCCCGACCCGTGGCGTACCAACCCGGTAGGCCGTTTCTGGGATCGCCTGCGTGGACGCGATGTCAcgc                                                                                                            <  1:629754/143‑1 (MQ=255)

                               gACAGTTATTTAATGTCGACGAATGGCGCGATCAGCTGAAGGCGATGCCAGAAGCAAAACGCTCCTCGATGTTTCCCGACCCGTGGCGTACCAACCCGGTAGGCCGTTTCTGGGATCGCCTGCGTGGACGCGATGTCAcgccg                                                                                                          <  1:393065/143‑1 (MQ=255)

                                aCAGTTATTTAAAGACGACGAAGGGCGCGATCAGCCGAAGGCGATGCCAGAAGCAAAACGCTCCTCGATGTTTCCCGACCCGTGGCGTACCAACCCGGTAGGCCTTTTCTGGGATCGCCTGCGTGGACGCGATGTCAcgccgc                                                                                                         <  1:248723/143‑1 (MQ=255)

                                   gTTAATTAAAGACGACGAAGGGCGCGATCAGCTGAAGGCGATGCCAGAAGCAAAACGCTCCTCGATGTTTCCCGACCCGTGGCGTACCAACCCGGTAGGCCTTTTCTGGGATCGCCCGCGGGGACGCGATGCCACGCCGCGCt                                                                                                      >  2:653170/1‑143 (MQ=255)

                                      aattaaAGACGACGAAGGGCGCGATCAGCTGAAGGCGATGCCAGAAGCAAAACGCTCCTCGATGTTTCCCGACCCGTGGCGTACCAACCCGGTAGGCCGTTTCTGGGATCGCCTGCGTGGACGCGATGTCACGCCGCGCTATc                                                                                                   >  2:194338/1‑143 (MQ=255)

                                        ttaaAGACGACGAAGGGCGCGATCAGCTGAAGGCGATGCCAGAAGCAAAACGCTCCTCGATGTTTCCCGACCCGTGGCGTACCAACCCGGTAGGCCGTTTCTGGGATCGCCTGCGTGGACGCGATGTCACGCCGCGCTATCTg                                                                                                 >  1:523056/1‑143 (MQ=255)

                                             gacgacGAAGGGCGCGATCAGCTGAAGGCGATGCCAGAAGCAAAACGCTCCTCGATGTTTCCCGACCCGTGGCGTACCAACCCGGTAGGCCTTTTCTGGGATCGCCTGCGTGGACGCGATGTCACGCCCCGCTCTCTGGCTcc                                                                                            >  2:386085/1‑142 (MQ=255)

                                                   gaAGGGCGCGATCAGCTGAAGGCGATGCCAGAAGCAAACCGCTCCTCGATGTTTCCCGACCCGTGGCGTACCAACCCGTTAGGCCTTTTCTGGGATCGCCTGCGTGGACGCGATGTCACGCCGCGCTATCTGGCTCGTTTGAc                                                                                      <  2:680125/143‑1 (MQ=255)

                                                       ggCGCGATCAGCTGAAGGCGATGCCAGAAGCAAAACGCTCCTCGAGGTTTCCCGACCCGTGGCGTACCAACCCGGTAGGCCTTTTCTGGGGTCGCCTGCGTGGACGCGATGTGACGCCGCGCTATCGGGCTGGTTTGaagcaa                                                                                  >  1:299194/1‑138 (MQ=255)

                                                           cgATCAGCTGAAGGCGATGCCAGAAGCAAAACGCTCCTCGATGTTTCCCGACCCGTGGCGTACCAACCCGGTAGGCCGTTTCTGGGATCACCTGCGTGGACGCGATGTCACGCCGCGCTATCTGGCTCGGTTGACCGaagaag                                                                              >  1:109162/1‑143 (MQ=255)

                                                              tCAGCTGAAGGCGATGCCAGAAGCAAATCGCTCCTCGATGTTTCCCGACCCGTGGCGTACCAACCCGGTAGGCCTTTTCTGGGATCGCCTGCGTGGACGCGATGTCACGCCGCGCTATCTGGCTCGTTTGACCAAAGAAGAGc                                                                           <  1:612882/143‑1 (MQ=255)

                                                                   agAAGGCGATGCCAGAAGCAAAACGCTGCTCGATGTTTCCCGACCCGTGGCGTACCAACCCGGTAGGCCGTTTCTGGGATCGCCTGCGTGGACGCGATGTCACGCCGCGCTATCTGGCTCGTTTGACCCAAGAAGAGCAGgag                                                                      >  1:483745/2‑143 (MQ=255)

                                                                    gAAGGCGATGCCAGAAGCAAAACGCTCCTCGATGTTTCCCGACCCGTGGCGTACCAACCCGGTAGGCCGTTTCTGGGATCGCCTGCGTGGACGCGCCGTCACGCCGCGCTATCTGACTCGTTTCACCACAGAAGAGccagaca                                                                     >  1:734954/1‑137 (MQ=255)

                                                                    gAAGGCGATGCCAGAAGCAAAACGCTCCTCGATGTTTCCCGACCCGTGGCGTACCAACCCGGTAGGCCGTTTCTGGGATCGCCTGCGTGGACGCGATGTCACGCCGCGCTATCTGGCTCGTTTGACCAAAGAAGAGCAGgaga                                                                     <  1:451970/143‑1 (MQ=255)

                                                                                agagGCAAAACGCTCCTGGTTGTTTCCCGACCCGTGGCGTGCCAACCCGGTAGGCCGTTTGTGGGATTGCCTGCGTGGACGCGATGTCACGCCGCGCTATCTGGCTCGTTTGACCAAAGAAGAGCAGGAGAGCGAGCAAAAGt                                                         <  2:394676/143‑1 (MQ=255)

                                                                                   aGCAAAACGCACACAGAAGTATCCCGACCCGTGGCGTACCAACCCGGTAGGCCGTTTCTGGGATCGCCTGCGTGGACGCGATGTCACGCCGCGCTATCTGGCTCGTTTGACCAAAGAAGAGCAGGAGAGCGAGCAAAAGTGGc                                                      <  1:166533/143‑1 (MQ=255)

                                                                                               ctcGATGGTTCCCGACCCGTGGCGTACCATCCCGGTAGGCCGTTTCTGGGATCGCTTGCGTGGACGCGATGTCACGCCGCGCTATCTGGCTCGTGTGACCAAAGAAGAGCAGGAGAGCGAGCAAAAGTGGCGTACCGTCGGTa                                          <  1:361239/143‑1 (MQ=255)

                                                                                                     gTTTCCCGCCCCGTGGCGTACCAACCCGGTAGGCTGTTTCTGTGATCGCCTGCGTGGACGCGATGTCACGCCGCGCTATCGGGCTCGTGAGACCAAAGAAGAGCAGGAGAGCGAGCAAAAGTGGCGTACCGTCGGTACCATcc                                    <  1:578856/143‑1 (MQ=255)

                                                                                                      tttCCCGACCCGTGGCGTACCAACCCGGTAGGCCTTTTCTGGGATCGCCTGCGTGGACGCGATGTCACGCCGCGCTATCTGGCTCGTTTGACCACAGAAGAACAAGAAAACGAGCAAAAGTGGCGTACCGTCGGTACAACccg                                   >  1:21544/1‑143 (MQ=255)

                                                                                                       ttgacgtcccGTGGCGTACCATCCGGGTACGCGGTTTCTGGGATCGCCTGCGTGGACGCGATGTCACGCCGCGCTATCTGGCTCGTTTGACCAAAGAAGAGCAGGAGAGCGAGCAAAAGTGGCGTACCGTCGGTACCATccgc                                  <  2:44954/136‑1 (MQ=255)

                                                                                                        tCCCGACCCGTGGCGTACCAACCCGGTAGGCTGTTTCTGGGATCGCCTGCGTGGACGCGATGTCACGCCGCGCTCTCTGGCTCGTTTCACCAAAGAAGAGCCGGAGACCCAGCAAAAGTGTCGTACAGCCACTCCCATccgcc                                 >  2:581932/1‑143 (MQ=255)

                                                                                                          cccaCCCGTGGCCTACCAACGCGTTAGGCGTTTTCTTGGATGGCGTGCGTGGACGCGATGTCACGCCGCGCTATCTGGCTCGTTTGACCAAAGAAGAGCAGGAGAGCGAGCAAAAGTGGCGTACCGTCGGTACCATCCGCCGt                               <  1:622357/140‑1 (MQ=255)

                                                                                                              cccGTGGCGTACCAACCCGGTAGGCCTTTTCTGGGATCGCCTGCGTGGACGCGATGTCACGCCGCGCTATCTGGCTCGTTTGACCAAAGAAGAGCAGGAGAGCGAGCAAAAGTGGCGTACCGTCGGTACCATCCGCCGTTACa                           <  1:583212/143‑1 (MQ=255)

                                                                                                                        aCCAACCCGGTAGGCCGTTTCTGGGATCGCCTGCGTGGACGCGATGTCACGCCGCGCTATCTGGCTCGTTTGACCAAAGAAGAGCAGGAGAGCGAGCAAAAGTGGCGTACCGTCGGTACCATCCGCCGTTACATTCTGTTGAt                 <  1:707462/143‑1 (MQ=255)

                                                                                                                             ccggggaGGCCGTTTCTGGGACCGCCTGCGGGGACGCGATGTCACGCCGCGCTATCTGGCTCGTTTGACCAAAGAAGAGCAGGAGAGCGAGCAAAAGTGGCGTACCGTCGGTACCATCCGCCGTTACATTCTGTTGATCCTGa            <  1:487724/137‑1 (MQ=255)

                                                                                                                                       cGTTTCTGGGATCGCCTGCGTGGACGCGATGTCACGCCGCGCTATCTGGCTCGTTTGACCAAAGAAGCGCAGCAGAGCGAGCAAAAGTGGCGTACCGTCGGTACCATCCGCCGTTACATTCTGTTGATCCTGACGCTCGCGCa  >  1:121906/1‑143 (MQ=255)

GAACAAGCCTGGCCAGATTCACTTGCTGATGGACAGTTAATTAAAGACGACGAAGGGCGCGATCAGCTGAAGGCGATGCCAGAAGCAAAACGCTCCTCGATGTTTCCCGACCCGTGGCGTACCAACCCGGTAGGCCGTTTCTGGGATCGCCTGCGTGGACGCGATGTCACGCCGCGCTATCTGGCTCGTTTGACCAAAGAAGAGCAGGAGAGCGAGCAAAAGTGGCGTACCGTCGGTACCATCCGCCGTTACATTCTGTTGATCCTGACGCTCGCGCA  >  NC_000913/1111028‑1111305

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A