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 F49 I1 R1	57	62.9	2678826	98.4%	2635964	146.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_002947_CJ‑RC	4,741,379	A→G	intergenic (+509/+244)	gltA → / ← yeiW	citrate synthase/putative oxidoreductase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947_CJ‑RC	4,741,379	0	A	G	97.4%	127.0 / ‑4.5	38	intergenic (+509/+244)	gltA/yeiW	citrate synthase/putative oxidoreductase
Reads supporting (aligned to +/- strand): ref base A (0/1); new base G (18/19); total (18/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.91e-01

GTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGAACCT‑CCGCCAACTGCAATTCGTGA‑ACCAAGCAAAAGGCCCCGAAAAGGCCCTCC‑GCAGCCCCCCCAACCTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGCCACTTGCCAGTT  >  NC_002947_CJ‑RC/4741244‑4741517

gTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGtcctcct                                                                                                                                 <  3:181231/148‑2 (MQ=255)

         tgCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGcgcctc                                                                                                                       >  7:345830/1‑147 (MQ=255)

             gcaCGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGcgcctcgacc                                                                                                                   >  8:239597/1‑143 (MQ=255)

             gcaCGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGcgcctcgacc                                                                                                                   >  4:168140/1‑143 (MQ=255)

                       aCGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAgcg                                                                                                         >  7:19869/1‑149 (MQ=255)

                       aCGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAgc                                                                                                          <  3:138378/148‑1 (MQ=255)

                           ggcgTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGACACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGgcgc                                                                                                     >  3:165605/1‑149 (MQ=255)

                            gcgTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGcc                                                                                                    <  6:147342/149‑1 (MQ=255)

                                 aCCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGAt                                                                                               >  6:277885/1‑149 (MQ=255)

                                  ccGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATc                                                                                              <  3:168140/149‑1 (MQ=255)

                                     gCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACg                                                                                           >  4:198166/1‑149 (MQ=255)

                                      ccATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTTCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACgg                                                                                          <  6:259936/149‑1 (MQ=255)

                                         tGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTca                                                                                       <  7:212715/149‑1 (MQ=255)

                                             gTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTAAGCAGCTACTACGAATTGCAA‑TCGAGA‑ATCCAGGCAAAGGCCCCGGACACGTCCTCCAGCAGCGCCACGACCTTGGCCAGCGGCGCCAAGATCACGGTCACAcc                                                                                   >  2:302778/1‑149 (MQ=255)

                                              tATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGtcctcctgcag                                                                                                                             <  1:246287/106‑6 (MQ=255)

                                              tATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGtcctcctgcag                                                                                                                             >  2:246287/1‑101 (MQ=255)

                                                ttGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACcgc                                                                                 >  8:163889/1‑148 (MQ=255)

                                                     cTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAgg                                                                           >  2:219136/1‑149 (MQ=255)

                                                      tGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGc                                                                          >  3:72719/1‑149 (MQ=255)

                                                        ggTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCACGGACACGTCCTCCTGCAGCGCCTCGCCCTTGGCCAGCGGCGCCTTGATAACGGTCACACCGCGATAGGCCt                                                                        >  5:195089/1‑149 (MQ=255)

                                                          tataGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGATTCCATGC‑ACAGGCACCGGAGACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGTTAGGCCtt                                                                       <  1:302778/148‑1 (MQ=255)

                                                          tataGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTg                                                                      <  6:277569/149‑1 (MQ=255)

                                                            taGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGt                                                                     <  4:21339/148‑1 (MQ=255)

                                                             aGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTa                                                                    <  8:345830/148‑1 (MQ=255)

                                                               gTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACtt                                                                 <  7:239597/149‑1 (MQ=255)

                                                                tCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACTCGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTg                                                                <  6:33984/149‑1 (MQ=255)

                                                                  cAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGa                                                              >  6:44618/1‑149 (MQ=255)

                                                                    gCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCGGACACGTCCTCCT‑GCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGAccc                                                           <  2:58298/149‑1 (MQ=255)

                                                                     ctctGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGAccc                                                           <  8:241477/149‑1 (MQ=255)

                                                                          gTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGTCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCa                                                      >  7:51080/1‑149 (MQ=255)

                                                                          gTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCa                                                      <  7:163889/149‑1 (MQ=255)

                                                                                                          ttgcaTTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGGGGGACACCTTGATCCcgtcctc                       >  8:201821/5‑149 (MQ=255)

                                                                                                            gcaTTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCcgtcctcg                      <  3:316388/146‑1 (MQ=255)

                                                                                                                          caggcacaGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGCCACtt         <  4:72719/141‑1 (MQ=255)

                                                                                                                          caggcacaGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGCCACtt         <  2:283544/141‑1 (MQ=255)

                                                                                                                               acaGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGCCACTTGCCAGt   >  5:212692/3‑149 (MQ=255)

                                                                                                                                caGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGCCACTTGCCAGtt  <  1:2745/148‑1 (MQ=255)

                                                                                                                                caGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATAACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGCCACTTGCCAGtt  >  1:317977/2‑149 (MQ=255)

GTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGAACCT‑CCGCCAACTGCAATTCGTGA‑ACCAAGCAAAAGGCCCCGAAAAGGCCCTCC‑GCAGCCCCCCCAACCTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCCTTGGCCACTTGCCAGTT  >  NC_002947_CJ‑RC/4741244‑4741517

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A