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
A10 F28 I1 R1	180	66.5	2263572	99.4%	2249990	138.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,563,545	G→A	intergenic (+428/‑47)	yffP → / → yffQ	CPZ‑55 prophage; uncharacterized protein YffP/CPZ‑55 prophage; uncharacterized protein YffQ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,563,545	0	G	A	94.9%	118.2 / ‑1.7	39	intergenic (+428/‑47)	yffP/yffQ	CPZ‑55 prophage; uncharacterized protein YffP/CPZ‑55 prophage; uncharacterized protein YffQ
Reads supporting (aligned to +/- strand): ref base G (1/1); new base A (18/19); total (19/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.75e-01

ATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAGATGTTGGTGATTACAGGCTGAACGGGGAGGA  >  NC_000913/2563409‑2563677

aTGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACtgatga                                                                                                                                   <  1:669376/140‑1 (MQ=255)

  gggAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGatgatg                                                                                                                                 <  2:174244/140‑1 (MQ=255)

    gAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGATGATGGt                                                                                                                               >  1:312654/1‑140 (MQ=255)

             tttGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGATGATGGTAATGTTGGt                                                                                                                      <  2:312654/140‑1 (MQ=255)

                gtgATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGATGATGGTAATGTTGGTTTg                                                                                                                   <  1:918694/140‑1 (MQ=255)

                      cAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTAt                                                                                                             >  1:374762/1‑140 (MQ=255)

                          tCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGATGATGGTAATGTTGGTTTGCTGTATTGaa                                                                                                         <  1:778348/140‑1 (MQ=255)

                          tCGCTTTTTCCCTTCAGGCATTTTTGTTTAATT‑AATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGATGATGGTAATGTTGGTTTGCTGTATTGAAc                                                                                                        <  2:1016758/140‑1 (MQ=255)

                                       tCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGATGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAggagga                                                                                            <  1:369198/140‑1 (MQ=255)

                                                         ttCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGATGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAAt                                                                          >  2:1102610/1‑140 (MQ=255)

                                                           caatcaaCGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGATGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCg                                                                        <  1:432439/140‑1 (MQ=255)

                                                             atcaaCGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGATGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCa                                                                      <  2:746216/140‑1 (MQ=255)

                                                              tcaaCGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGATGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCaa                                                                     >  2:58408/1‑140 (MQ=255)

                                                              tcaaCGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGATGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCaa                                                                     >  2:902107/1‑140 (MQ=255)

                                                                   gAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGATGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAatcatc                                                                >  2:997739/1‑140 (MQ=255)

                                                                       ggCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGATGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGa                                                            <  1:997739/140‑1 (MQ=255)

                                                                           gTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGATGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGt                                                        >  2:189277/1‑140 (MQ=255)

                                                                           gTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGATGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGt                                                        <  1:1102610/140‑1 (MQ=255)

                                                                            ttCCCAACAACAAAATAAAGATGGGAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGATGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTg                                                       >  2:744996/1‑140 (MQ=255)

                                                                                      caaAATAAAGATGGGAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGATGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGgtg                                             >  1:1040114/1‑140 (MQ=255)

                                                                                      caaAATAAAGATGGGAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGATGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGgtg                                             >  2:84559/1‑140 (MQ=255)

                                                                                      caaAATAAAGATGGGAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGATGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGgtg                                             >  1:515316/1‑140 (MQ=255)

                                                                                      caaAATAAAGATGGGAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGATGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGgtg                                             >  1:674726/1‑140 (MQ=255)

                                                                                              aGATGGGAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGATGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGtttgcttt                                     >  1:992390/1‑140 (MQ=255)

                                                                                                  gggAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGATGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAg                                 <  1:58408/140‑1 (MQ=255)

                                                                                                   ggAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGATGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAGa                                >  1:828828/1‑140 (MQ=255)

                                                                                                   ggAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGATGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAGa                                >  2:381336/1‑140 (MQ=255)

                                                                                                     aGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGATGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAGATg                              <  1:744996/140‑1 (MQ=255)

                                                                                                     aGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGATGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAGATg                              <  2:992390/140‑1 (MQ=255)

                                                                                                     aGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGATGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAGATg                              <  2:828828/140‑1 (MQ=255)

                                                                                                     aGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGATGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAGATg                              <  1:902107/140‑1 (MQ=255)

                                                                                                         aaaaaTGAAACGGTGGGAAGTGGCTTTACTGATGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAGATGTTgg                          <  1:84559/140‑1 (MQ=255)

                                                                                                         aaaaaTGAAACGGTGGGAAGTGGCTTTACTGATGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAGATGTTgg                          <  2:1040114/140‑1 (MQ=255)

                                                                                                             aTGAAACGGTGGGAAGTGGCTTTACTGATGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAGATGTTGGTGAt                      >  1:995408/1‑140 (MQ=255)

                                                                                                              tGAAACGGTGGGAAGTGGCTTTACTGATGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAGATGTTGGTGAtt                     <  1:985444/140‑1 (MQ=255)

                                                                                                               gAAACGGTGGGAAGTGGCTTTACTGATGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAGATGTTGGTGATTa                    <  2:986039/140‑1 (MQ=255)

                                                                                                                 aaCGGTGGGAAGTGGCTTTACTGATGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAGATGTTGGTGATTACa                  >  1:525639/1‑140 (MQ=255)

                                                                                                                      tGGGAAGTGGCTTTACTGATGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAGATGTTGGTGATTACAGGCTg             >  1:169647/1‑140 (MQ=255)

                                                                                                                       gggAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAGATGTTGGTGATTACAGGCTGa            <  2:374762/140‑1 (MQ=255)

                                                                                                                                cTTTACTGATGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAGATGTTGGTGATTACAGGCTGAACGGggagg   >  2:91927/1‑140 (MQ=255)

                                                                                                                                 tttACTGATGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAGATGTTGGTGATTACAGGCTGAACGGggagga  <  2:863269/140‑1 (MQ=255)

ATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAGATGTTGGTGATTACAGGCTGAACGGGGAGGA  >  NC_000913/2563409‑2563677

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