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
A14 F1 I1 R1	770	68.5	3470224	91.7%	3182195	103.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,789,683	C→T	W133* (TGG→TGA)	waaH ←	LPS(HepIII)‑glucuronic acid glycosyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,789,683	0	C	T	77.3%	69.6 / 21.8	44	W133* (TGG→TGA)	waaH	LPS(HepIII)‑glucuronic acid glycosyltransferase
Reads supporting (aligned to +/- strand): ref base C (5/5); new base T (20/14); total (25/19)
Fisher's exact test for biased strand distribution p-value = 7.23e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.24e-01

CACGGCGATAAACCCCCATCCAGACAACGTGAGTCCAACGGCGCGAAGAAAGCCCCATCCGCAGCCAGTCCGGGCCGGTTAATACGCCGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGCCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCGTTGCACTGCGCCACGTCGAGGTCGTCCTCTAACGCCATGGTCATCAGCGTTTCGTACATGGTGGGATAGACTTCATCGTCAGCATCGACAAA  >  NC_000913/3789562‑3789811

cACGGCGATAAACCCCCATCCAGACAACGTGAGTCCAACGGCGCGAAGAAAG‑CCCATCCGCAGCCAGTCCGGGCCGGTTAATACGCCGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGTCAGGTTTCTCCCGTTTCa                                                                                                                >  1:564649/1‑139 (MQ=255)

  cGGCGATAAACCCCCATCCAGACAACGTGAGTCCAACGGCGCGAAGAAAGCCCCATCCGCAGCCAGTCCGGGCCGGTTAATACGCCGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGTCAGGTTTCTCCCGTTTCAc                                                                                                               >  1:1563584/1‑139 (MQ=255)

        tAAACCCCCATCCAGACAACGTGAGTCCAACGGCGCGAAGAAAG‑CCCATCCGCAGCCAGTCCGGGCCGGTTAATACGCCGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGTCAGGTTTCTCCCGTTTCACGAAAaca                                                                                                        <  2:564649/139‑1 (MQ=255)

                  tCCAGACAACGTGAGTCCAACGGCGCGAAGAAAGCCCCATCCGCAGCCAGTCCGGGCCGGTTAATACGCCGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGTCAGGTTTCTCCCGTTTCACGAAAACACCAGt                                                                                                   >  1:731180/1‑135 (MQ=255)

                  tCCAGACAACGTGAGTCCAACGGCGCGAAGAAAGCCCCATCCGCAGCCAGTCCGGGCCGGTTAATACGCCGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGTCAGGTTTCTCCCGTTTCACGAAAACACCAGt                                                                                                   <  2:731180/135‑1 (MQ=255)

                  tCCAGACAACGTGAGTCCAACGGCGCGAAGAAAGCCCCATCCGCAGCCAGTCCGGGCCGGTTAATACGCCGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGTCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGc                                                                                               >  1:240629/1‑139 (MQ=255)

                      gACAACGTGAGTCCAACGGCGCGAAGAAAGCCACATCCGCAGCCAGTCCGGGCCGGTTAATACGCCGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGCCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCGTTg                                                                                           >  2:179523/1‑139 (MQ=255)

                       aCAACGTGAGTCCAACGGCGCGAAGAAAGCCCCATCCGCAGCCAGTCCGGGTCGGTTAATACGCCGGTTGAGCAAATGCGATCGGTGGGGATGGATTGTCAGGTTTCTCCCGTTTCACGAAAACGCCAGTCAGCGTTGc                                                                                          >  1:1062465/1‑139 (MQ=255)

                         aaCGTGAGTCCAACGGCGCGAAGAAAGCCCCATCCGCAGCCAGTCCGGGCCGGTTAATACGCCGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGTCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCGTTGCAc                                                                                        >  1:1513389/1‑139 (MQ=255)

                          aCGTGAGTCCAACGGCGCGAAGAAAGCCCCATCCGCAGCCAGTCCGGGCCGGTTAATACGCCGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGTCAGGTTTCTTCCGTTTCACGAAAACACCAGTCAGCGTTGCACt                                                                                       <  2:240629/139‑1 (MQ=255)

                              gAGTCCAACGGCGCGAAGAAAGCCCCATCCGCAGCCAGTCCGGGCCGGTTAATACGCCGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGTCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCGTTGCACTgcgc                                                                                   <  1:1136357/139‑1 (MQ=255)

                                 tCCAACGGCGCGAAGAAAGCCCCATCCGCAGCCAGTCCGGGCCGGTTAATACGCCGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGTCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCGTTGCACTGCGCCAc                                                                                >  1:392336/1‑139 (MQ=255)

                                 tCCAACGGCGCGAAGAAAGCCCCATCCGCAGCCAGTCCGGGCCGGTTAATACGCCGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGCCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCg                                                                                              >  2:1169046/1‑125 (MQ=255)

                                 tCCAACGGCGCGAAGAAAGCCCCATCCGCAGCCAGTCCGGGCCGGTTAATACGCCGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGCCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCg                                                                                              <  1:1169046/125‑1 (MQ=255)

                                   cAACGGCGCGAAGAAAGCCCCATCCGCAGCCAGTCCGGGCCGGTTAATACGCCGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGTCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCGTTGCACTgcgc                                                                                   >  2:464199/1‑134 (MQ=255)

                                   cAACGGCGCGAAGAAAGCCCCATCCGCAGCCAGTCCGGGCCGGTTAATACGCCGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGTCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCGTTGCACTgcgc                                                                                   <  1:464199/134‑1 (MQ=255)

                                         cgcgAAGAAAGCCCCATCCGCAGCCAGTCCGGGCCGGTTAATACGCCGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGCCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCGTTGCACTGCGCCACGTCGAGgt                                                                        >  2:1109199/1‑139 (MQ=255)

                                           cgAAGAAAGCCCCATCCGCAGCCAGTCCGGGCCGGTTAATACGCCGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGTCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCGTTGCACTGCGCCACGTCGAGgtcg                                                                      <  2:1563584/139‑1 (MQ=255)

                                                        aTCCGCAGCCAGTCCGGGCCGGTTAATACGCCGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGTCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCGTTGCACTGCGCCACGTCGAGGTCGTCCTCTAACGCCa                                                         >  1:1196389/1‑139 (MQ=255)

                                                              aGCCAGTCCGGGCCGGTTAATACGCCGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGCCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCGTTGCACTGCGCCACGTCGAGGTCGTCCTCTAACGCCATGGtca                                                   <  1:179523/139‑1 (MQ=255)

                                                                  aGTCCGGGCCGGTTAATACGCCGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGTCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCGTTGCACTGCGCCACGTCGAGGTCGTCCTCTAACGCCATGGTCATCAg                                               <  2:1354233/139‑1 (MQ=255)

                                                                    tCCGGGCCGGTTAATACGCCGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGTCAGGTTTCTCCCGTTTCAc                                                                                                               <  2:478762/73‑1 (MQ=255)

                                                                    tCCGGGCCGGTTAATACGCCGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGTCAGGTTTCTCCCGTTTCAc                                                                                                               >  1:478762/1‑73 (MQ=255)

                                                                    tCCGGGCCGGTTAATACGCCGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGTCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCGTTGCACTGCGCCACGTCGAGGTCGTCCTCTAACGCCATGGTCATCAGCg                                             >  2:1130760/1‑139 (MQ=255)

                                                                    tCCGGGCCGGTTAATACGCCGGTTGAGCGAAGGCGATCGGCGGGGATGGATTGTCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCGTTGCACTGCGCCACGTCGAGGTCGTCCTCTAACGCCATGGTCATCAGCg                                             >  2:620454/1‑139 (MQ=255)

                                                                          ccGGTTAATACGCCGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGTCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCGTTGCACTGCGCCACGTCGAGGTCGTCCTCTAACGCCATGGTCATCAGCGtt                                           >  1:1603281/1‑135 (MQ=255)

                                                                          ccGGTTAATACGCCGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGTCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCGTTGCACTGCGCCACGTCGAGGTCGTCCTCTAACGCCATGGTCATCAGCGtt                                           <  2:1603281/135‑1 (MQ=255)

                                                                          ccGGTTAATACGCCGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGTCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCGTTGCACTGCGCCACGTCGAGGTCGTCCTCTAACGCCATGGTCATCAGCGTTTCGt                                       >  2:603972/1‑139 (MQ=255)

                                                                             gTTAATACGCCGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGTCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCGTTGCACTGCGCCACGTCGAGGTCGTCCTCTAACGCCATGGTCATCAGCGTTTCGTACa                                    >  1:370276/1‑139 (MQ=255)

                                                                                  tACGCCGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGTCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCGTTGCACTGCGCCACGTCGAGGTCGTCCTCTAACGCCATGGTCATCAGCGTTTCGTACAtggtg                               <  1:603972/139‑1 (MQ=255)

                                                                                    cGCCGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGTCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCGTTGCACTGCGCCACGTCGAGGTCGTCCTCTAACGCCATGGTCATCAGCGTTTCGTACATGGTggg                             <  2:1513389/139‑1 (MQ=255)

                                                                                       cGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGTCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCGTTGCACTGCGCCACGTCGAGGTCGTCCTCTAACGCCATGGTCATCAGCGTTTCGTACATGGTGGGATa                          >  2:363521/1‑139 (MQ=255)

                                                                                       cGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGCCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCGTTGCACTGCGCCACGTCGAGgtcg                                                                      <  2:1245479/95‑1 (MQ=255)

                                                                                       cGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGCCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCGTTGCACTGCGCCACGTCGAGgtcg                                                                      >  1:1245479/1‑95 (MQ=255)

                                                                                       cGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGCCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCGTTGCACTGCGCCACGTCGAGGTCGTCCTCTAACGCCATGGtcatca                                                <  2:765866/117‑1 (MQ=255)

                                                                                       cGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGCCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCGTTGCACTGCGCCACGTCGAGGTCGTCCTCTAACGCCATGGtcatca                                                >  1:765866/1‑117 (MQ=255)

                                                                                          ttGAGCGAAGGCGATCGGTGGGGATGGATTGTCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCGTTGCACTGCGCCACGTCGAGGTCGTCCTCTAACGCCATGGTCATCAGCGTTTCGTACATGGTGGGATAGAc                       >  1:1449409/1‑139 (MQ=255)

                                                                                                   ggCGATCGGTGGGGATGGATTGTCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCGTTGCACTGCGCCACGTCGAGGTCGTCCTCTAACGCCATGGTCATCAGCGtt                                           <  2:1375294/110‑1 (MQ=255)

                                                                                                   ggCGATCGGTGGGGATGGATTGTCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCGTTGCACTGCGCCACGTCGAGGTCGTCCTCTAACGCCATGGTCATCAGCGtt                                           >  1:1375294/1‑110 (MQ=255)

                                                                                                    gCGATCGGTGGGGATGGATTGTCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCGTTGCACTGCGCCACGTCGAGGTCGTCCTCTAACGCCATGGTCATCAGCGTTTCGTACATGGTGGGATAGACTTCATCGTCa             >  2:590854/1‑139 (MQ=255)

                                                                                                        tCGGTGGGGATGGATTGTCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCGTTGCACTGCGCCACGTCGAGGTCGTCCTCTAACGCCATGGTCATCAGCGTTTCGTACATGGTGGGATAGACTTCATCGTCAGCAt         >  1:315559/1‑139 (MQ=255)

                                                                                                             ggggATGGATTGTCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCGTTGCACTGCGCCACGTCGAGGTCGTCCTCTAACGCCATGGTCATCAGCGTTTCGTACATGGTGGGATAGACTTCATCGTCAGCATCGACa    <  2:392336/139‑1 (MQ=255)

                                                                                                             ggggATGGATTGTCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCGTTGCACTGCGCCACGTCGAGGTCGTCCTCTAACGCCATGGTCATCAGCGTTTCGTACATGGTGGGATAGACTTCATCGTCAGCATCGACa    <  2:1449409/139‑1 (MQ=255)

                                                                                                               ggatggatTTCCAGGTTTCTCCCGTTTCACGAAACCACCAGTCAGCGTTGCACTGCGCCACGTCGAGGTCGTCCTCTAACGCCATGGTCATCAGCGTTTCGTACATGGTGGGATAGACTTCATCGTCAGCATCGACaaa  <  1:1109199/139‑1 (MQ=255)

CACGGCGATAAACCCCCATCCAGACAACGTGAGTCCAACGGCGCGAAGAAAGCCCCATCCGCAGCCAGTCCGGGCCGGTTAATACGCCGGTTGAGCGAAGGCGATCGGTGGGGATGGATTGCCAGGTTTCTCCCGTTTCACGAAAACACCAGTCAGCGTTGCACTGCGCCACGTCGAGGTCGTCCTCTAACGCCATGGTCATCAGCGTTTCGTACATGGTGGGATAGACTTCATCGTCAGCATCGACAAA  >  NC_000913/3789562‑3789811

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A