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
A17 F25 I0 R1	13	19.6	632057	98.4%	621944	146.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,089,622	A→G	11.5%	W278R (TGG→CGG)	rhaT ←	L‑rhamnose:proton symporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	4,089,622	0	A	G	11.5%	73.6 / 4.4	35	W278R (TGG→CGG)	rhaT	L‑rhamnose:proton symporter
Reads supporting (aligned to +/- strand): ref base A (17/14); new base G (2/2); total (19/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.51e-01

TCAACACCGTTACCGGACGGCGTCCTGCATTGTTCCACTCTTTCAGCACCAGCCCGACGATACCGCCGCACAATACATAGAAACTCATATGCAGCATCCAACTGATGTAGTCATACTGCGCCGGAATGCGGGCGTGGCCCCAGGCATAGAAAAAGAATTGCAGATACCACATCAACCCGCCCAGTGTCGAGAGTAACACATTGTGAATGATCAGCGATTTTGCCAGCGAGAAGTCGGCTTTTAGCGACAAATCCTTCACTTTTGCCAGACGAATAAAACAGAAACCGAG  >  CP009273/4089481‑4089769

tCAACACCGTTACCGGACGGCGTCCTGCATTGTTCCACTCTTTCAGCACCAGCCCGACGATACCGCCGCACAATACATAGAAACTCATATGCAGCATCCAACTGATGTAGTCATACTTCGCCGGAATGCGGGCGTGGCCCCAg                                                                                                                                                    <  2:162963/143‑1 (MQ=255)

    cacCGGTACCGGCCGGCGTCCTGCATTGTGCCACTCTTTCAGCACCAGCCCGACGATACCGCCGCACAATACATAGAAACTCATATGCAGCATCCAACTGATGTAGTCATACTGCGCCGGAATGCGGGCGTGGCCCCAGGCATAGaaaa                                                                                                                                          <  1:83199/149‑1 (MQ=255)

     acCGTGACCGGACGGCGTCCGGCATTGTTCCACTCTTTCAGCACCAGCCCGACGATACCGCCGCACAATACATAGAAACTCATATGCAGCATCCAACTGATGTAGTCATACTGCGCCGGAATGCGGGCGTGGCCCCAGGCATa                                                                                                                                               <  2:258428/143‑1 (MQ=255)

       cGTTACCGGTCGGCGTCCTGCATTGTTCCACTCTTTCAGCACCAGCCCGACGATACCGCCGCACAATACATAGACACTCATATGCAGCATCCAACTGATGTAGTCAGACTGCGCCGGAATGCGGGCGTGGCCCCAGGCATAGAAAAAGa                                                                                                                                       <  1:160653/149‑1 (MQ=255)

            ccGGACGGCGTCCTGCATTGTTCCACTCTTTCAGCACCAGCCCGACGATACCGCCGCACAATACATAGAAACTCATATGCAGCATCCAACTGATGTAGTCATACTGCGCCGGAATGCGGGCGTGGCCCCAGGCATAGAAAAAg                                                                                                                                        <  2:125221/143‑1 (MQ=255)

                 cGGCGTCCTTCATTGTTCCACTCTTGCAGCACCAGCCCGACGATACCGCCGCACAATACATAGAAACTCATATGCAGCATCCAACTGATGTAGTCATACTGCGCCTTAATGCGGGCGTGGCCCCAGGCATAGAAAAAGAATTg                                                                                                                                   <  2:273216/143‑1 (MQ=255)

                         tGCATTGTTCCACTCTTTCAGCACCAGCCCGACGATACCGCCGCACAATACATAGAGACTCATATGCAGCATCCAACTGATGTAGTCATACTGCGCCGGAATGCGGGCGTGGCCCCAGGCATAGAAAAAGAATTGCAgttcacacctca                                                                                                                     >  1:65458/1‑138 (MQ=255)

                                  ccACTCTTTCAGCACCAGCCCGACGTTCCCGCCGCACAATACATAGAAACGCATATGCGGCATCCAACTTATGTAGTCGTACTGAGCCGGAAGGCGGGCGTGGCCCCAGGCATAGAAAAAGAATTGCAGATACCACATCAAcc                                                                                                                  >  2:211526/1‑143 (MQ=255)

                                    aCTCTTTCAGCACCAGCCCGACGATACCGCCGCACAATACATAGAAACTCATATGCAGCATCCAACTGATGTAGTCATACTGCGCCGGAATGCGGGCGTGGCCCCAGGCATAGAAAAAGAATTGCAGATACCACATCAACCCGCCCAgt                                                                                                          >  1:110203/1‑149 (MQ=255)

                                              cACCAGCCCGACGATACCGCCGCACAATACATAGAAACTCATATGCAGCATCCAAGTGATGTAGTCATACTGCGCCGGAATGCGGGCGTGGCCCCAGGCATAGAAAAAGAATTGCAGATGCCACATCACACCGCCCAggggcg                                                                                                      >  2:187841/1‑138 (MQ=255)

                                               aCCAGCCCGACGATACCGCCGCACAATACATAGAAACTCATATGCAGCATCCAACTGATGTAGTCATACTGCGCCGGAATGCGGGCGTGGCCCCAGGCATAGAAAAAGAATTGCAGATACCACATCAACCCGCCCAGTGTCGGGAGaaa                                                                                               >  1:151390/1‑149 (MQ=255)

                                                  aGCCCGACGATACCGCCGCACAATACATAGAAACTCATATGCAGCATCCAACTGATGTAGTCATACTGCGCCGGAATGCGGGCGTGGCCCCGGGCATAGAAAAAGAATTGCAGATACCACATCAACCCGCCCAGTGTCgaggg                                                                                                  >  2:138822/1‑141 (MQ=255)

                                                  aGCCCGACGATACCGCCGCACAATACATAGAAACTCATATGCAGCATCCAACTGATGTAGTCATACTGCGCCGGAATGCGGGCGTGGCCCCGGGCATAGAAAAAGAATTGCAGATACCACATCAACCCGCCCAGTGTCGagag                                                                                                  >  2:56790/1‑143 (MQ=255)

                                                         cgaTACCGCCGCACAACACATAGAAACTCATATGCAGCATCCAACTGATGTAGTCATACTGCGCCGGAATGCGGGCGTGGCCCCAGGCATAGAAAAAGAATTGCAGATACCACATCAACCCGCCCAGTGTCGAGAGTAAcaca                                                                                           <  2:20698/143‑1 (MQ=255)

                                                             aCCGCCGCACAATACATAGAAACTCATATGCAGCATCCAACTGATGTAGTCATACTGCGCCGGAATGCGGGCGTGGCCCCAGGCATAGAAAAAGAATTGCAGATACCACATCAACCCGCCCAGTGTCGAGAGTAACACATTGTGAATGa                                                                                 <  1:268133/149‑1 (MQ=255)

                                                                 ccgcACAATACATAGAAACTCATATGCAGCATCCAACTGATGTAGTCATACTGCGCCGGAATGCGGGCGTGGCCCCAGGCATAGAAAAAGAATTGCAGATACCACATCAACCCGCCCAGTGTCGAGAGTAACACATTGTGAATGATCAg                                                                             <  1:69621/149‑1 (MQ=255)

                                                                 ccgcACAATACATAGAAACTCATATGCAGCATCCAACTGATGTAGTCATACTGCGCCGGAATGCGGGCGTGGCCCCAGGCATAGAAAAAGAATTGCAGATACCACATCAACCCGCCCAGTGTCGAGAGTAACACATTGTGAATGATCAg                                                                             <  1:69717/149‑1 (MQ=255)

                                                                            aTAGAAACTCATATGCAGCATCCAACTGATGTAGTCATACTGCGCCGGAATGCGGGCGTGGCCCCAGGCATAGAAAAAGAATTGCAGATACCACATCAACCCGCCCAGTGTCGAGAGTAACACATTGTGAATGATCAGCGATTTTGCCa                                                                  >  1:261822/1‑149 (MQ=255)

                                                                              aGAAACTCATATGCAGCATCCAACTGATGTAGTCATACTGCGCCGGAATGCGGGCGTGACCCCAGACATAGAAAAAGAATTGCAGATACCCCACCAACCCGCCCAGTGTCGCGAGTAACACATTGTGAATGATCAGGGAGTTTGcaacc                                                                >  1:205294/1‑145 (MQ=255)

                                                                                      atatGCAGCATCCAACTGATGTAGTCATACTGCGCCGGAATGCGGGCGTGGCCCCAGGCATAGAAAAAGAATTGCAGATACCACATCAACCCGCCCAGTGTCGAGAGTAACACATGGTGAATGATCAGCGATTTTGCCAGCGAGAAggc                                                        >  1:141144/1‑147 (MQ=255)

                                                                                              caTCCAACTGATGTAGTCATACTGCGCCGGAATGCGGGCGTGGCCCCAGGCATAGAAAAAGAATTGCAGATACCACATCAACCCGCCCAGTGTCGAGAGTAACACATTGTGAATGATCAGCGATTTTGCCAGCGAGAAGTCgg                                                      <  2:261255/143‑1 (MQ=255)

                                                                                               aTCCAACTGATGTAGTCATACTGCGCCGGAATGCGGGCGTGGCCCCAGGCATAGAAAAAGAATTGGAGATACCACATCAACCCGCCCAGTGTCGAGAGTAACACATTGTGAATGATCAGCGATTTTGCCAGCGAGAAGTCGGCttttcg                                               >  1:73037/1‑147 (MQ=255)

                                                                                                tCCAACTGATGTAGTCATACTGCGCCGGAATGCGGGCGTGGCCCCAGGCATAGAAAAAGAATTGCAGATACCACATCAACCCGCCCAGTGTCGAGAGTAACACATTGTGAATGATCAGCGATTTTGCCAGCGAGAAGTCGGCt                                                    <  2:136796/143‑1 (MQ=255)

                                                                                                           caGTCATACTGCGCCGGAATGCGGGCGTGGCCCCAGGCATAGAAAAAGAATTGCAGATACCACATCAACCCGCCCAGTGTCGAGAGTAACACATTGTGAATGATCAGCGATTTTGCCAGCGAGAAGTCGGCTTTTAGCGACAAATCCtt                                   <  1:97905/148‑1 (MQ=255)

                                                                                                              tCATACTGCGCCGGAATGCGGGCGTGGCCCCAGGCATAGAAAAAGAATTGCAGATACCACATCAACCCGCCCAGGGTCGAGAGTACCACATTGTGAGTGATCAGCGATTTGGCCAGCGAGCAGTCGGCTTTTAGCGACAAATc                                      >  2:105198/1‑143 (MQ=255)

                                                                                                                 tACTGCGCCGGAATGCGGGCGTGGCCCCAGGCATAGAAAAAGAATTGCAGATACCACATCAACCCGCCCAGAGTCGAGAGTAACACATTGTGAATGATCAGCGATTTTGCCAGCGAGAAGTCGGCTTTTAGCGACAAATCCTTCACttt                             >  1:212523/1‑149 (MQ=255)

                                                                                                                    tGCGCCGGAATGCGGGCGTGGCCCCGGGCATAGAAAAAGAATTGCAGATACCACATCAACCCGCCCAGTGTCGAGAGTAACACATTGTTAATGATCAGCGATTTTGCCAGCGCGAAGTCGGCTTTTAGCGACAAATCCTTCACTTTTGc                          <  1:63729/149‑1 (MQ=255)

                                                                                                                    tGCGCCGGAATGCGGGCGTGGCCCCGGGCATAGAAAAAGAATTGCAGAACCAACCGCAACCCGCCCAGTGTCGAGAGTAACACATTGTGAATGATCAGCGATTTTGCCAGCGAGAAGTCGGCTTTTAGCGACAAATCCTTCACTTTTGc                          <  1:158451/149‑1 (MQ=255)

                                                                                                                        ccGGAATGCGGGCGTGGCCCCAGGCATAGAAAAAGAATTGCAGATACCACATCAACCCGCCCAGTGTCGAGAGTAACACATTGTGAATGATCAGCGATTTTGCCAGCGAGAAGTCGGCTTTTAGCGACAAATCCTTCACTTTTGCCAGa                      >  1:122309/1‑149 (MQ=255)

                                                                                                                          gtaaTGCGGGCGTGGCCCCAGGCATAGAGAAAGAATTGCAGATACCACATCAACCCGCCCAGTGTCGGGAGTAACACATTGTGAATGATCAGCGATTTTGCCAGCGAGAAGGCGGCTTTTAGCGACAAAACCTTCACTTTTGc                          >  2:2384/3‑143 (MQ=255)

                                                                                                                               gCGGGCGTGGCCCCAGGCATCGAAAAAGAATTGCAGATACCACATCAACCCGCCCAGTGTCGAGAGTAACACATTGTGAATGATCAGCGATTATGCCAGCGAGAAGTCGGCTTTTGGCGACAAATCCTTCACTTTGGCCGGAc                     >  2:210841/1‑143 (MQ=255)

                                                                                                                                 gggCGTGGCCCCAGGCATAGAAAAAGAATTGCAGATACCACATCAACCCGCCCAGTGTCGAGAGTAACACATTGTGAATGATCAGCGATTTTGCCAGCGAGAAGTCGGCTTTTAGCGACAAATCCTTCACTTTTGCCAGACGAATaaaa             >  1:237840/1‑149 (MQ=255)

                                                                                                                                   gCGTGGCCCCAGGCATAGAAAAAGAATTGCAGATACCACATCAACCCGCCCAGTGTCGAGAGTAACACATTGTGAATGATCAGCGATTTTGCCAGCGAGAAGTCGGCTTTTAGCGACAAATCCTTCACTTTTGCAAGACGAAGacaaca           >  1:245975/1‑149 (MQ=255)

                                                                                                                                          cccAGGCATAGAAAAAGAATTGCAGATACCACATCAACCCGCCCAGTGTCGAGAGTAACACATTGTGAATGATCAGCGATTTTGCCAGCGAGAAGTCGGCTTTTAGCGACAAATCCTTCACTTTTGCCAGACGAATAAAACAGAAACCg    <  1:91559/149‑1 (MQ=255)

                                                                                                                                            cAGGCATAGAAAAAGAATTGCAGATACCACATCAACCCGCCCAGTGTCGAGAGTAACACATTGTGAATGATCAGCGATTTTGCCAGCGTGAAGTCGGCTTTTAGCGACAAATCCTTCACTTTTGCCAGACGAATAAAACAGAAACCGAg  >  1:242235/1‑149 (MQ=255)

TCAACACCGTTACCGGACGGCGTCCTGCATTGTTCCACTCTTTCAGCACCAGCCCGACGATACCGCCGCACAATACATAGAAACTCATATGCAGCATCCAACTGATGTAGTCATACTGCGCCGGAATGCGGGCGTGGCCCCAGGCATAGAAAAAGAATTGCAGATACCACATCAACCCGCCCAGTGTCGAGAGTAACACATTGTGAATGATCAGCGATTTTGCCAGCGAGAAGTCGGCTTTTAGCGACAAATCCTTCACTTTTGCCAGACGAATAAAACAGAAACCGAG  >  CP009273/4089481‑4089769

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A