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
A14 F8 I1 R1	16	57.5	2022698	92.3%	1866950	143.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_tpiA	4,111,596	G→A	L179L (CTG→TTG)	yiiQ ←	DUF1454 family putative periplasmic protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_tpiA	4,111,596	0	G	A	97.4%	109.3 / ‑3.9	39	L179L (CTG→TTG)	yiiQ	DUF1454 family putative periplasmic protein
Reads supporting (aligned to +/- strand): ref base G (0/1); new base A (23/14); total (23/16)
Fisher's exact test for biased strand distribution p-value = 3.95e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.34e-01

AAAGGAAGATGGCCGCCCCGCAGGGCAGCAGGTCTGTGAAACAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAGCCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGC  >  NC_000913_3_pae_tpiA/4111451‑4111736

aaaTGAAGATGGCCGCCCCGCAGGGTGGCAGGTCTCGCAAACAGTCTAGAGCTTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCTCCAGCTTAATCGGTTCAACAGCGAAGGTCAAccc                                                                                                                                           <  1:893870/149‑1 (MQ=255)

  aGGAAGATGGCCGCTCCGCAGGGCAGCAGGTCTGTGGAACAGGATCGAGATTCCTCGGCACAAAGGCTTTGCTTTTTGTTATTTATTCAACCCTTCAAGCGCTTCAGCTAGCGCCTGCTTAATCCGTTGAACATCGAAGGTCAAccccc                                                                                                                                         >  2:836292/1‑148 (MQ=255)

   ggAAGATGGCCGCCCCGCAGGGCAGCAGGTCTGTGAAACAGTATAGAGATTCATCGGCACAAAAGCATTGCTTTGTGTTATTGCCTCCAACCACCAGGCTTTGCAGTGAGGGCCATTTTAATCGGTTCAACACCGATGTCCAACCCCtt                                                                                                                                        >  2:468310/1‑149 (MQ=255)

     aaGATGGCCGCCCCGCAGGGCAGCGGGGCTGTGAAACAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCtttt                                                                                                                                      <  2:134417/149‑1 (MQ=255)

               ccccGCAGGGCAGCAGGTCTGTGAAACAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCg                                                                                                                                 <  2:841600/144‑1 (MQ=255)

               ccccGCAGGGCAGCAGGTCTGTGAAACAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCg                                                                                                                                 >  1:841600/1‑144 (MQ=255)

                    aaGGGCAGACGGTCCGTGAAACAGTATAGATATTCATCGGCTGAAAGGTTTTGCTTTGTGTCATTTATTCAAACCTTCAAGCGATGCAGCTAGCGCTAGCTTAATCGGTTCAATAGCGAAGGTCAACACCTTTTCGCCGTTGCCTGCGa                                                                                                                       <  2:303267/148‑1 (MQ=255)

                       ggCAGCAGGTCTGTGAAACAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTGAACCCCTTTTCGCCGTTGTCCGCGaaac                                                                                                                    >  1:61320/1‑146 (MQ=255)

                       ggCAGCAGGTCTGTGAAACAGTATAGAGAATCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGacaa                                                                                                                    <  2:908108/149‑1 (MQ=255)

                                  tgtgAAACAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACTTAACGCAGt                                                                                                         >  2:745077/1‑149 (MQ=255)

                                  tgtgAAACAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGt                                                                                                         >  2:856962/1‑149 (MQ=255)

                                     gAAACAGTCTAGAGTTTCTTCGGCATCAAGGCTTTGCTTTTTGTAATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAGCCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCa                                                                                                      <  1:210247/149‑1 (MQ=255)

                                             ataGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTg                                                                                                        >  2:916389/1‑139 (MQ=255)

                                             ataGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTg                                                                                                        <  1:916389/139‑1 (MQ=255)

                                                     tCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGgtgt                                                                                      >  2:527405/1‑149 (MQ=255)

                                                       aTCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACGTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACCCAGGGCCCCTTCTGTCTCGTTGtat                                                                                    >  2:616716/1‑148 (MQ=255)

                                                        tCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGtaat                                                                                   >  2:777238/1‑149 (MQ=255)

                                                           gcaacaaGGCATTGGTTTTTGTGATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCCGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTATTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAAc                                                                                <  1:151482/144‑1 (MQ=255)

                                                             acaAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAAcc                                                                                                                                            <  2:371013/87‑1 (MQ=255)

                                                                      ttgctttTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACGCGTTTTCGCCGTTCCCAACACTGACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTc                                                                     >  1:447217/1‑149 (MQ=255)

                                                                      ttgctttTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTc                                                                     <  1:178180/149‑1 (MQ=255)

                                                                      ttgctttTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTc                                                                     <  1:683264/149‑1 (MQ=255)

                                                                                tCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTta                                                           >  1:810159/1‑149 (MQ=255)

                                                                                  aTTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAATGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGCAATAACGTTTGTTTTTACCCACCGCtagt                                                         >  2:166631/1‑149 (MQ=255)

                                                                                  aTTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTAAATCGGTTCACCAGCCAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACCACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTCCCCCTCCGTtcgt                                                         >  2:623139/1‑149 (MQ=255)

                                                                                               ttCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTCGTCGCGACTggcttt                                            >  1:437698/1‑144 (MQ=255)

                                                                                                        ttCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTc                                       >  1:247419/1‑145 (MQ=255)

                                                                                                        ttCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTc                                       <  2:247419/145‑1 (MQ=255)

                                                                                                             gtggagcCAGCTTAATCGGTCCACGCGCAAAGGTCATCCCCTTTTTGCTGTATTCCGCGCCAACATAACGTCGTGCACCTTCTGTCTCGTTGTAATAACGTTTGTTTTTCCCCGCCGTTCGTCGCGACTTCAGTTTTTTCTGGCTTtgt                              <  2:68197/144‑1 (MQ=255)

                                                                                                                  gcCAGCTTAATCGGTTCAACACCGAAGGTCAACCCCTTCTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGtttt                         >  2:889720/1‑149 (MQ=255)

                                                                                                                   ccAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTg                        >  2:841797/1‑149 (MQ=255)

                                                                                                                            tCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTact               >  1:337906/1‑147 (MQ=255)

                                                                                                                            tCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTCTTCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAGCGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTTTGGCTTTGTAGTTTGCTCCTTact               >  2:427152/1‑147 (MQ=255)

                                                                                                                                ttCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTg                                                                                                        <  2:1003713/56‑1 (MQ=255)

                                                                                                                                ttCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTg                                                                                                        >  1:1003713/1‑56 (MQ=255)

                                                                                                                                   aaCAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGa        <  1:777238/149‑1 (MQ=255)

                                                                                                                                    aCAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAg       >  2:135127/1‑149 (MQ=255)

                                                                                                                                      aGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACCACCTGACGCATTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAgtg     >  1:496689/1‑149 (MQ=255)

                                                                                                                                         gAAGGGCAACCCCTTTTCGCCGTTGTCCGCGACAACATACCGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGc  <  1:318116/149‑1 (MQ=255)

AAAGGAAGATGGCCGCCCCGCAGGGCAGCAGGTCTGTGAAACAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAGCCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGC  >  NC_000913_3_pae_tpiA/4111451‑4111736

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A