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
A16 F7 I1 R1	16	44.4	1557844	93.4%	1455026	142.3

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	94.6%	106.8 / NA	37	L179L (CTG→TTG)	yiiQ	DUF1454 family putative periplasmic protein
Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (23/12); minor base C (0/2); total (23/14)
Fisher's exact test for biased strand distribution p-value = 1.37e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGAAGATGGCCGCCCCGCAGGGCAGCAGGTCTGTGAAACAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAGCCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGC  >  NC_000913_3_pae_tpiA/4111454‑4111736

ggAAGATGGCCGCCCCGCAGGGCAGCAGGTCTGTGAAACAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCtt                                                                                                                                        >  1:493919/1‑149 (MQ=255)

   aGATGCCCCCCCCGCAGCGCAGCAGGTCTGAGAAACAGTACAGAGAATCATCGGCACAAAGGCTTTGCTTTTTGTCATTTACACAAACCTTCAACCTCTTCAGATAGCGCCAGCTTAATCGGCTCAACAGCGAAGGTCAACCCCTTTTc                                                                                                                                     <  1:381277/149‑1 (MQ=255)

         ccgccCCGCAGGGCAGCAGGTCTGTGAAACAGTATCGAGATTCATCGGCACAAAGGCTTTGCTATTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAACGAAGGTCAACCCAATTTCGcaagg                                                                                                                               >  2:356350/1‑145 (MQ=255)

         ccgccCCGCAGGGCAGCAGGTCTGTGAAACAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGtt                                                                                                                               <  2:60803/149‑1 (MQ=255)

                gCAGGGCAGCAGGTCTGTGAAACAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAACGAATGTCAACCCCTTTTCGCCGTTGTCcgcg                                                                                                                        >  2:239593/1‑149 (MQ=255)

                       agcagGTCTGTGAAACAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACAt                                                                                                                 >  1:516735/1‑149 (MQ=255)

                         cagGTCTGTGTAACAGTATAGAGATTCATCGGCACAAAGGCTTTGTTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCATCTTAATCGGTTCCACTGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATaa                                                                                                               <  1:23914/149‑1 (MQ=255)

                            gTCTGTGAAACAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCAATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTGGCCGTTGTCCGCGGCACCATacgcc                                                                                                            >  1:25239/1‑145 (MQ=255)

                             tCTGTGAAACAGTATAGAGATTCATCGGCACAACGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCa                                                                                                           >  2:710040/1‑149 (MQ=255)

                               tgtgAACCAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGt                                                                                                         >  2:268413/1‑149 (MQ=255)

                               tgtgAAACAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCAACAACATAACGCGGt                                                                                                         >  1:105044/1‑149 (MQ=255)

                                      cAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCtt                                                                                                  <  2:43485/149‑1 (MQ=255)

                                       aGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATACAGATAGCGCCAGTGTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTc                                                                                                 <  1:692003/149‑1 (MQ=255)

                                        gTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCATTAATCCCGTTTGCCGCGACAACATAACGCAGTGCACCTTCt                                                                                                <  1:579164/149‑1 (MQ=255)

                                                       ggCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGtaataa                                                                                 <  1:742864/149‑1 (MQ=255)

                                                           caAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACgtt                                                                             >  1:609334/1‑149 (MQ=255)

                                                             aaGGCTTTGCTTTTTCTCACTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACgtttg                                                                           >  2:640880/1‑149 (MQ=255)

                                                                gctttgctttTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCCGTGCACCTTCTGTCTCGGTGTACTAACgtttgttt                                                                        >  2:95108/1‑149 (MQ=255)

                                                                  tttgctttTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGttttt                                                                      <  1:566286/149‑1 (MQ=255)

                                                                   ttgctttTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTc                                                                     >  1:2726/1‑149 (MQ=255)

                                                                           tGTAATTTGTTCAAACCTTCATCCGATTCAGGTCGTGCCTTCTTAATCGGTTCAACAGCCAACGTCCCCCTCTTTTCGCCGTTGTCCGCGCCAACATACCGCCGTGCACCTCCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGt                                                             <  2:493919/149‑1 (MQ=255)

                                                                                tttATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTtagta                                                        >  2:39010/1‑149 (MQ=255)

                                                                                tttATTCAAACCTTCAAGCAATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACATTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTtagta                                                        >  1:459360/1‑149 (MQ=255)

                                                                                       aaaCCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCgcccg                                                 >  2:452845/1‑145 (MQ=255)

                                                                                        aaCCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGGCTGc                                                >  1:55407/1‑149 (MQ=255)

                                                                                           cTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGt                                             >  2:396458/1‑149 (MQ=255)

                                                                                            ttgaaGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGGGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGtt                                            >  2:402959/4‑149 (MQ=255)

                                                                                                      tCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGATTGTTTTTCCACGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCt                                  <  1:695908/149‑1 (MQ=255)

                                                                                                        aGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCttt                                <  1:39010/149‑1 (MQ=255)

                                                                                                          aTAGCGCCAGCTTAATCGGTTCAACAGCGCAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGTGTTtgg                              >  1:315484/1‑148 (MQ=255)

                                                                                                                 cAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCAGCCGTTAGTAGCACATGCTGTTTTTTCTGACTTTGTGtttttg                       >  2:113669/1‑147 (MQ=255)

                                                                                                                          cGGGTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGGGACAAAATACCGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATg              <  1:95108/149‑1 (MQ=255)

                                                                                                                           gtttCAACAGCGACGGTCACCCCCTTGTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATgg             <  1:27701/147‑1 (MQ=255)

                                                                                                                                  cAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTgtgt                            <  2:625153/127‑1 (MQ=255)

                                                                                                                                  cAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTgtgt                            >  1:625153/1‑127 (MQ=255)

                                                                                                                                     cGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGtgtg   >  1:464150/1‑149 (MQ=255)

                                                                                                                                      gAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCGGTCTCGGTGGAATAACGTTTGTTTTTCCCCGCCGTTCGTAGCGACTGCAGTTTTTTCTGGCCTTGTGTTTGGTGCATTAATGGGGTGatgggga  >  1:328058/1‑143 (MQ=255)

GGAAGATGGCCGCCCCGCAGGGCAGCAGGTCTGTGAAACAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAGCCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGC  >  NC_000913_3_pae_tpiA/4111454‑4111736

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