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
A1 F104 I0 R1	54	57.6	1336546	96.4%	1288430	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,018,612	G→A	100%	R103* (CGA→TGA)	mgt ←	Monofunctional glycosyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,018,612	0	G	A	95.1%	124.1 / ‑1.3	41	R103* (CGA→TGA)	mgt	Monofunctional glycosyltransferase
Reads supporting (aligned to +/- strand): ref base G (2/0); new base A (15/24); total (17/24)
Fisher's exact test for biased strand distribution p-value = 1.66e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.79e-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.

ACGATCATTATCATAAAAATAATTTTTGACAACTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCGTTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGATAAAAAATACATGATA  >  USA300TCH1516_ALE/2018475‑2018742

aCGATCATTATCATAAAAATAATTTTTGACAACTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTc                                                                                                                                 >  1:200615/1‑141 (MQ=255)

       ttATCATAAAAATAATTTTTGACAACTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTcc                                                                                                                          >  2:212119/1‑141 (MQ=255)

                 aataatTTTTGACAACTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATaa                                                                                                                <  1:535496/141‑1 (MQ=255)

                  ataatTTTTGACAACGTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATaaa                                                                                                               <  1:98360/141‑1 (MQ=255)

                      tttttGTCAACTTGTTGTGTAATGGTACTATCACCTTGCACAGCTCTGTTGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCa                                                                                                           <  2:515195/141‑1 (MQ=255)

                       ttttGACAACTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGTTAATCGTTGAAAATAAAGCTCTAGTTCTACCTTTCAAATCGAATCCATGATGATTGTAGAATCACTCATCTTCCATTGAAATAAAGGCAc                                                                                                          <  2:168999/141‑1 (MQ=255)

                           gACAACTTGTTGTGTAATGGTACTACCACCTTGCCCATCTCTGTCGCTAATCGTTGACAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCttt                                                                                                      <  2:487802/141‑1 (MQ=255)

                                cTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACAt                                                                                                 <  1:552355/141‑1 (MQ=255)

                                cTTGTTGTGTAATGGTACTACCACCTTGCACACCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACAt                                                                                                 <  2:448882/141‑1 (MQ=255)

                                         tAATGGTACTACCACCTTTCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTCTAACATACTCTGGCa                                                                                        <  1:335215/141‑1 (MQ=255)

                                             gggactccCACCTTGCACAGCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGATTCATTCATCTTCCATTGAAATAAATGCACCTTTAACATACTCTGGCATGtt                                                                                    <  2:471619/138‑1 (MQ=255)

                                             ggTACTACCACCTTGCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGtt                                                                                    <  2:544364/141‑1 (MQ=255)

                                                actacCACCTTGCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATc                                                                                 >  1:220790/1‑141 (MQ=255)

                                                      accTTGCACATCTCTGTCGCTAGTCGGTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGa                                                                           >  1:490841/1‑141 (MQ=255)

                                                      accTTGCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGa                                                                           >  1:210796/1‑141 (MQ=255)

                                                              caTCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGTCATGTTATCAGCTGACACACAac                                                                   >  2:542705/1‑141 (MQ=255)

                                                                 ctctGTCGCTAATTGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAactac                                                                <  2:281602/141‑1 (MQ=255)

                                                                    tGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACttt                                                             <  1:306196/141‑1 (MQ=255)

                                                                          tcaTCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTAtttt                                                       <  2:283354/139‑1 (MQ=255)

                                                                          tAATCGTTGAAAATAAAGCTCTAGTTGTACCGTTCAAATCGCATCCATGATGATTGTAGAATCATCCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTAtttt                                                       <  2:604802/141‑1 (MQ=255)

                                                                              cGTTGAAAATAAAGCTCTAGTTTTACCTTTCAAATCGTATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAAt                                                   <  2:26849/141‑1 (MQ=255)

                                                                                ttGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAAttt                                                 <  1:427920/141‑1 (MQ=255)

                                                                                   aaaaTAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAACGGCAAAACTTTCAGACTCTGGCATGTTCTCTTCTAACACAAAACTACTTTTATTTTCAATTTTTc                                              <  2:640282/141‑1 (MQ=255)

                                                                                      aTAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTa                                           <  1:212657/141‑1 (MQ=255)

                                                                                       tAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAg                                          <  1:505327/141‑1 (MQ=255)

                                                                                       aaaaGCCCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAg                                          <  1:61797/140‑1 (MQ=255)

                                                                                         aaGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCGTTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTGTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAGtt                                        >  2:295348/1‑141 (MQ=255)

                                                                                             tctAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAGTTCATc                                    >  2:353149/1‑141 (MQ=255)

                                                                                                  ttGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCCTGTTATCAGCTGACACAATACGACTGTTATTTTCAATTTTTCTTAGTTCATCCACAt                               <  2:294767/141‑1 (MQ=255)

                                                                                                     tACCTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAGTTCATCCACATTAt                            >  1:501742/1‑141 (MQ=255)

                                                                                                       ccTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAGTTCATCCACATTATcg                          >  2:525600/1‑141 (MQ=255)

                                                                                                       ccTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAGTTCATCCACATTATcg                          <  1:212119/141‑1 (MQ=255)

                                                                                                       ccTTTCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTGTCTTAGTTCATCCACATTATcg                          >  2:358115/1‑141 (MQ=255)

                                                                                                          ttCAAATCGAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACCAAACTACTTTTATTTTCAATTTTTCTTAGTTCATCCACATTATCGCgt                       >  2:274856/1‑141 (MQ=255)

                                                                                                                  gAATCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCTATTTTTCTTAGTTCATCCACATTATCGCGTGTGGATaa               >  1:243740/1‑141 (MQ=255)

                                                                                                                    aTCCGTGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTAATTTTATTTTACCTCTTCCTTAGTTCCTCCACATTATCGCGTGTAGATaaaa             >  2:138740/1‑141 (MQ=255)

                                                                                                                    aTCCATGATGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGATaaaa             <  1:439678/141‑1 (MQ=255)

                                                                                                                      ccATGAAGATTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTGCAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGATaaaaaa           <  2:235858/141‑1 (MQ=255)

                                                                                                                           atgatTGTAGAATCATTCATCTTCCATTGAAATAAAGGCAACTTTAGCATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGATAAAAAATACAt      >  1:130158/1‑141 (MQ=255)

                                                                                                                            tgatTGTAGAATCATTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGATAAAAAATACATg     >  1:563427/1‑141 (MQ=255)

                                                                                                                               ttGTAGAATCGTTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGATAAAAAATACATGATa  >  1:192240/1‑141 (MQ=255)

ACGATCATTATCATAAAAATAATTTTTGACAACTTGTTGTGTAATGGTACTACCACCTTGCACATCTCTGTCGCTAATCGTTGAAAATAAAGCTCTAGTTGTACCTTTCAAATCGAATCCATGATGATTGTAGAATCGTTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGATAAAAAATACATGATA  >  USA300TCH1516_ALE/2018475‑2018742

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A