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
A5 F178 I0 R1	41	49.4	1100758	95.6%	1052324	140.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,416,458	A→T	100%	I216N (ATT→AAT)	oppD_4 ←	Oligopeptide transport ATP‑binding protein OppD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,416,458	0	A	T	98.0%	129.1 / ‑5.4	44	I216N (ATT→AAT)	oppD_4	Oligopeptide transport ATP‑binding protein OppD
Reads supporting (aligned to +/- strand): ref base A (0/0); major base T (21/22); minor base G (1/0); total (22/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.74e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTG  >  USA300TCH1516_ALE/1416326‑1416590

aCTCAATGGTAGTAAGCCCTCTTTATTTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTg                                                                                                                               <  2:83077/140‑1 (MQ=255)

 cTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGCCGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCGCGTTCAATGATTTGACATTCTTTTAAAACATAATTGTACTGa                                                                                                                              >  2:312539/1‑140 (MQ=255)

      tCATAGTAATCCCTTTTTAATTGTGTTCTATATTTAATTTGGCGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAata                                                                                                                         <  1:110742/140‑1 (MQ=255)

      tCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAata                                                                                                                         <  1:110707/140‑1 (MQ=255)

      tCATAGGAATCCCTCGTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAata                                                                                                                         <  2:213958/140‑1 (MQ=255)

       cATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATTCTCATACTTGAAATGATTAATATTACCTCATTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAatat                                                                                                                        >  1:478867/1‑140 (MQ=255)

        ttattattCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATAtt                                                                                                                       <  2:427887/133‑1 (MQ=255)

           gTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATAATTAATATTACCTAGTTCAATGATTTGACCTTCTTTTAAAACATATTTATACTGTAAATATTTCa                                                                                                                    >  1:288157/1‑140 (MQ=255)

           ctAATCCCTCTTTTATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTTAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCa                                                                                                                    <  2:80966/139‑1 (MQ=255)

                    ctTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGAc                                                                                                           >  2:4268/1‑140 (MQ=255)

                       tAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTa                                                                                                        >  1:288674/1‑140 (MQ=255)

                          ttGTGTTCTATATTTAATTAGACGTTCAGTAAACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGt                                                                                                     <  1:414203/140‑1 (MQ=255)

                          tgttgtTCTTTATTTAATTAGCCGTTCAGCTTACGGATGAAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGt                                                                                                     <  1:41552/137‑1 (MQ=255)

                                     atTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACAAAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGata                                                                                          >  1:420056/1‑140 (MQ=255)

                                         aaTTAGTGGTTCAGTATACGCATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGAtaataa                                                                                      <  2:316352/140‑1 (MQ=255)

                                               aCGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCTTTCAATGATTTGACCTTCTTTTAAAAAATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATg                                                                                >  1:193310/1‑140 (MQ=255)

                                                       tataCGGATGCAAATGCTCATACTTGAAATGATTAATCTTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGTCATTCTTTCAATACATTACTTAAGTTATGTATGATAATAAATAATGTTTGACCa                                                                        >  1:108087/1‑140 (MQ=255)

                                                       tataCGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTTACCTTCTTTTAAAACATAATTGTAATGAAAATATAGAAATACATGACTTACGTTATGTGTGATAATAAATAATGTTTTACCa                                                                        >  1:209302/1‑140 (MQ=255)

                                                       tataCGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATAACTTAAGTAATGTGTGATAATAAATAATGTTTGACCa                                                                        >  2:130292/1‑140 (MQ=255)

                                                         taCGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTTAGCGATCTAATTAATAATGTTTGACCATg                                                                      <  2:118387/140‑1 (MQ=255)

                                                         aactgttGCAAATGCTCATACTTGAAATCATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATg                                                                      <  2:408874/134‑1 (MQ=255)

                                                           cGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGtt                                                                    >  2:513910/1‑140 (MQ=255)

                                                            ggATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGCCTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTc                                                                   <  2:413907/140‑1 (MQ=255)

                                                                  aaaTGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATAc                                                             <  1:479068/140‑1 (MQ=255)

                                                                    aTGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACaa                                                           >  1:60023/1‑140 (MQ=255)

                                                                         cATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGc                                                      <  2:288927/140‑1 (MQ=255)

                                                                          aTACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTGCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTAACCATGTTCTAATACataatgat                                                     >  2:414287/1‑133 (MQ=255)

                                                                            aCTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCCATACATGCCTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAAAATGCTGt                                                   >  1:250749/1‑140 (MQ=255)

                                                                                   aTGATTAATAGTACCTCGTTCCTTGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAAt                                            <  2:98726/140‑1 (MQ=255)

                                                                                     gATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATcc                                          <  1:253006/140‑1 (MQ=255)

                                                                                      aTTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCa                                         <  1:169817/140‑1 (MQ=255)

                                                                                      aTTAACATTACTGCGTTAAATTATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCa                                         <  1:535532/140‑1 (MQ=255)

                                                                                                ccTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTTTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGAtt                               <  1:55809/140‑1 (MQ=255)

                                                                                                 cTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTa                              >  1:462977/1‑140 (MQ=255)

                                                                                                  tCGTTCAATGATTTGACCTTCTTTTACAACTTAAGTTTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTAc                             >  1:266690/1‑140 (MQ=255)

                                                                                                    gTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATATGAGATAATAAATAATGTTTGAACATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCg                           >  1:59156/1‑140 (MQ=255)

                                                                                                     ttCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTCATAAATCCATCACTTGATTACCGt                          >  2:300109/1‑140 (MQ=255)

                                                                                                     tgtgacgATTTGACCTTGTTGTAAAACATAATTGTCCTGACAATATTTCAATACATGATTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATCAATCCATCACTTGATTACCGt                          <  2:32198/134‑1 (MQ=255)

                                                                                                      tCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGCCTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTCATTACCGtt                         >  2:331874/1‑140 (MQ=255)

                                                                                                        aaTGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCa                       >  1:499900/1‑140 (MQ=255)

                                                                                                                        tttAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGc       <  2:60753/140‑1 (MQ=255)

                                                                                                                          tAAAACAGAATGGTACTGACAATATTTCAATCTATGACTTAAGTTATGTGTGAGAATAAATAATGTTTGGCCATGTTCTAATACAATATGCAGTAATAAATCCATCACTTGATTACCGTACAAAGCATCTAATGATTCaa     >  2:459923/1‑140 (MQ=255)

                                                                                                                            aaaCATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACt   >  2:403722/1‑140 (MQ=255)

                                                                                                                             aaCATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATTCAATGATGCAACTg  <  1:359488/140‑1 (MQ=255)

ACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTG  >  USA300TCH1516_ALE/1416326‑1416590

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