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	4,172,011	(C)_6→7	intergenic (+255/‑46)	rrfB → / → murB	5S ribosomal RNA/UDP‑N‑acetylenolpyruvoylglucosamine reductase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,172,005	1	.	C	95.0%	130.8 / ‑0.3	40	intergenic (+249/‑52)	rrfB/murB	5S ribosomal RNA/UDP‑N‑acetylenolpyruvoylglucosamine reductase
Reads supporting (aligned to +/- strand): ref base . (1/1); new base C (21/17); total (22/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑T‑CCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTAAAACCCTGGAACACATTTGGCATTGATCATAATGCTCAGCACATTGTATGTGCCGAAGACGAACAAC  >  NC_000913/4171867‑4172138

tGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑T‑c                                                                                                                                      >  2:141390/1‑140 (MQ=255)

  cGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑T‑ccc                                                                                                                                    >  1:184390/1‑140 (MQ=255)

   aaaGCAGCGGCGGGGGGGGGGGGGGGAAGCCCCCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑T‑cccc                                                                                                                                   <  2:302644/139‑1 (MQ=21)

                      tGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑TCCCCCCCACAGATACGGTAAACt                                                                                                                 >  2:729641/1‑140 (MQ=255)

                       ggCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑TCCCCCCCACAGATACGGTAAACTa                                                                                                                >  2:673107/1‑140 (MQ=255)

                                gACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGttt                                                                                                       >  2:522447/1‑140 (MQ=255)

                                    cccgccATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGc                                                                                                   >  1:27169/1‑140 (MQ=255)

                                      cgccATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCAt                                                                                                 <  1:729641/140‑1 (MQ=255)

                                              aCTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAag                                                                                         <  1:223055/140‑1 (MQ=255)

                                              aCTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAag                                                                                         <  2:184390/140‑1 (MQ=255)

                                                                 aGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCtt                                                                      >  1:140646/1‑140 (MQ=255)

                                                                   cAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTaa                                                                    <  2:598723/140‑1 (MQ=255)

                                                                   cAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTaa                                                                    <  2:27169/140‑1 (MQ=255)

                                                                            aTCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTAAAACCCTGGa                                                           >  2:647874/1‑140 (MQ=255)

                                                                             tCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTAAAACCCTGGaa                                                          >  1:887766/1‑140 (MQ=255)

                                                                                  aCGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTAAAACCCTGGAACACAt                                                     >  1:372290/1‑140 (MQ=255)

                                                                                     gATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTAAAACCCTGGAac                                                         <  1:239433/133‑1 (MQ=255)

                                                                                     gATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTAAAACCCTGGAac                                                         >  2:239433/1‑133 (MQ=255)

                                                                                        ggCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTAAAACCCTGGaa                                                          <  1:468059/129‑1 (MQ=255)

                                                                                        ggCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTAAAACCCTGGaa                                                          <  1:623453/129‑1 (MQ=255)

                                                                                        ggCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTAAAACCCTGGaa                                                          >  2:623453/1‑129 (MQ=255)

                                                                                        ggCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTAAAACCCTGGaa                                                          >  2:468059/1‑129 (MQ=255)

                                                                                        ggCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTAAAACCCTGGAACACATTTGGCa                                               >  1:405287/1‑140 (MQ=255)

                                                                                        ggCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTAAAACCCTGGAACACATTTGGCa                                               >  1:110151/1‑140 (MQ=255)

                                                                                        ggCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTAAAACCCTGGAACACATTTGGCa                                               <  2:193340/140‑1 (MQ=255)

                                                                                         gCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTAAAACCCTGGAACACATTTGGCAt                                              <  1:522447/140‑1 (MQ=255)

                                                                                         gCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTAAAACCCTGGAACACATTTGGCAt                                              <  1:673107/140‑1 (MQ=255)

                                                                                         gCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTAAAACCCTGGAACACATTTGGCAt                                              >  2:341916/1‑140 (MQ=255)

                                                                                         gCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTAAAACCCTGGAACACATTTGGCAt                                              >  2:431490/1‑140 (MQ=255)

                                                                                         gCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑T‑CCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTAAAACCCTGGAACACATTTGGCAtt                                             >  1:150398/1‑140 (MQ=255)

                                                                                          ccTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTAAAACCCTGGAACACATTTGGCAtt                                             <  1:341916/140‑1 (MQ=255)

                                                                                              tttGCGTATCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTAAAACCCTGGAACACATTTGGCATTGATc                                         >  2:95876/1‑140 (MQ=255)

                                                                                                         aCAAACTCTTCCTGTCGTCATATCTACAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTAAAACCCTGGAACACATTTGGCATTGATCATAATGCTCAg                              <  2:372290/140‑1 (MQ=255)

                                                                                                          cAAACTCTTCCTGTCGTCATATCTACAAGCCACC‑CCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTAAAACCCTGGAACACATTTGGCATTGATCATAATGCTCAGc                             <  1:871902/140‑1 (MQ=255)

                                                                                                            aaCTCTTCCTGTCGTCATATCTACAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTAAAACCCTGGAACACATTTGGCATTGATCATAATGCTCAGcac                           <  2:405287/140‑1 (MQ=255)

                                                                                                             aCTCTTCCTGTCGTCATATCTACAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTAAAACCCTGGAACACATTTGGCATTGATCATAATGCTCAGcaca                          <  1:647874/140‑1 (MQ=255)

                                                                                                                      gtcgtcATATCTACAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTAAAACCCTGGAACACATTTGGCATTGATCATAATGCTCAGCACATTGTAtgtg                 >  1:282373/1‑140 (MQ=255)

                                                                                                                       tcgtcATATCTACAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTAAAACCCTGGAACACATTTGGCATTGATCATAATGCTCAGCACATTGTATGTGc                >  2:624030/1‑140 (MQ=255)

                                                                                                                                  aCAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTAAAACCCTGGAACACATTTGGCATTGATCATAATGCTCAGCACATTGTATGTGCCGAAGACGaac     <  1:197949/140‑1 (MQ=255)

                                                                                                                                   cAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTAAAACCCTGGAACACATTTGGCATTGATCATAATGCTCAGCACATTGTATGTGCCGAAGACg        >  2:246904/1‑136 (MQ=255)

                                                                                                                                   cAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTAAAACCCTGGAACACATTTGGCATTGATCATAATGCTCAGCACATTGTATGTGCCGAAGACg        <  1:246904/136‑1 (MQ=255)

                                                                                                                                   cAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTAAAACCCTGGAACACATTTGGCATTGATCATAATGCTCAGCACATTGTATGTGCCGAAGACGaa      <  2:46256/138‑1 (MQ=255)

                                                                                                                                   cAAGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTAAAACCCTGGAACACATTTGGCATTGATCATAATGCTCAGCACATTGTATGTGCCGAAGACGaa      >  1:46256/1‑138 (MQ=255)

                                                                                                                                     aGCCA‑TCCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTAAAACCCTGGAACACATTTGGCATTGATCATAATGCTCAGCACATTGTATGTGCCGAAGACGaacaac  >  2:687905/1‑140 (MQ=255)

TGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCA‑T‑CCCCCCACAGATACGGTAAACTAGCCTCGTTTTTGCATCAGGAAAGCAGCTATGAACCACTCCTTAAAACCCTGGAACACATTTGGCATTGATCATAATGCTCAGCACATTGTATGTGCCGAAGACGAACAAC  >  NC_000913/4171867‑4172138

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `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