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
A8 F1 I2 R1	97	53.3	2484976	94.5%	2348302	111.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,594,132	(C)_8→9	pseudogene (3856/3861 nt)	yneO ←	pseudogene, AidA homolog

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,594,124	1	.	C	88.9%	145.0 / 10.7	45	pseudogene (2/1461 nt)	yneO	pseudogene, AidA homolog
Reads supporting (aligned to +/- strand): ref base . (2/3); new base C (16/24); total (18/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

CATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑G‑‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCC  >  NC_000913/1593991‑1594256

catcaGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑G‑‑ccccc                                                                                                                                  >  1:92050/1‑139 (MQ=255)

 atcaGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑G‑‑cccccc                                                                                                                                 >  2:700158/1‑139 (MQ=255)

 agcaGGCCATTGTTTCCGGTATAGTTGACGTTAACGGTCAGGACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGCCACGCAGT‑G‑‑cccccc                                                                                                                                 <  2:1215853/137‑1 (MQ=255)

      gCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑G‑‑ccccccc‑ccag                                                                                                                           <  2:1068187/139‑4 (MQ=255)

         aTTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑G‑‑cccccc                                                                                                                                 >  2:176905/1‑131 (MQ=255)

         aTTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑G‑‑cccccc                                                                                                                                 <  1:176905/131‑1 (MQ=255)

          ttGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GC‑CCCCCCC‑CAGGCAt                                                                                                                        >  2:1106765/1‑139 (MQ=255)

              ttCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GC‑CCCCCCC‑CAGGCATAACg                                                                                                                    <  1:726690/139‑1 (MQ=255)

                ccGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GC‑CCCCCCC‑CAGGCATAACGtt                                                                                                                  >  1:1112612/1‑139 (MQ=255)

                          tGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GC‑CCCCCCC‑CAGGCATAACGTTCATATCACCt                                                                                                        <  1:161828/139‑1 (MQ=255)

                              gTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GC‑CCCCCCC‑CAGGCATAACGTTCATATCAc                                                                                                          <  1:710965/133‑1 (MQ=255)

                              gTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GC‑CCCCCCC‑CAGGCATAACGTTCATATCAc                                                                                                          >  2:710965/1‑133 (MQ=255)

                              gTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑G‑‑ccccccc‑c                                                                                                                              >  1:1014877/1‑112 (MQ=255)

                              gTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑G‑‑ccccccc‑c                                                                                                                              <  2:1014877/112‑1 (MQ=255)

                              gTTAACCGTCAGTACATTCCCCGGTTTCCCCCCTTCCCTATTCATTTGAACCGTGCCCCCATTCTCCAGCTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GCCCCCCCCC‑CAGGCATAACGTTCATATCACCTGCa                                                                                                     <  2:268273/139‑1 (MQ=255)

                                  aCGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GC‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAgtggt                                                                                                <  1:700158/139‑1 (MQ=255)

                                   cGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑G‑‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGa                                                                                              <  2:785110/139‑1 (MQ=255)

                                          tACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GC‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTc                                                                                        >  2:370010/1‑139 (MQ=255)

                                           aCATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GC‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTcc                                                                                       <  1:831404/139‑1 (MQ=255)

                                              ttCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GC‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGa                                                                                    <  2:1112612/139‑1 (MQ=255)

                                               tCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GC‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGAc                                                                                   >  1:470522/1‑139 (MQ=255)

                                                ccccGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑G‑‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACAt                                                                                 >  2:1041545/1‑139 (MQ=255)

                                                   cGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GC‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATca                                                                               <  1:569062/139‑1 (MQ=255)

                                                    ggTTTCCCCCCTTCGCTATTCATTTGCACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑G‑‑CCCCCCCTCACGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATcac                                                                              >  1:575706/1‑139 (MQ=255)

                                                        tCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GC‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCa                                                                                                     <  2:392019/112‑1 (MQ=255)

                                                        tCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GC‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCa                                                                                                     >  1:392019/1‑112 (MQ=255)

                                                        tCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GC‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCg                                                                          <  2:405043/139‑1 (MQ=255)

                                                        tCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GC‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCg                                                                          <  2:151195/139‑1 (MQ=255)

                                                        tCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GC‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCg                                                                          <  2:1108430/139‑1 (MQ=255)

                                                        tCCCCCCTTCGCTATTCATTTGAACCGTACCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTATCGACACGCAGT‑GC‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCg                                                                          <  1:426306/139‑1 (MQ=255)

                                                           ccccTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GC‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTg                                                                       >  1:1088682/1‑139 (MQ=255)

                                                             ccTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GC‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGtt                                                                     <  2:1146254/139‑1 (MQ=255)

                                                               ttCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GC‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTAt                                                                   <  1:1106765/139‑1 (MQ=255)

                                                                      ttCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTCC‑‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATAtt                                                            <  2:525967/139‑1 (MQ=255)

                                                                              aaCCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GC‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGtt                                                    <  2:470522/139‑1 (MQ=255)

                                                                                ccGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑G‑‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGAc                                                 <  1:1041545/139‑1 (MQ=255)

                                                                                  gTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GC‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACt                                                >  2:124566/1‑139 (MQ=255)

                                                                                   tGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GC‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCg                                                                          <  1:389158/112‑1 (MQ=255)

                                                                                   tGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GC‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCg                                                                          >  2:389158/1‑112 (MQ=255)

                                                                                    gccgccATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GC‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCacac                                                                            <  2:676308/109‑1 (MQ=255)

                                                                                    gccgccATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GC‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCacac                                                                            >  1:676308/1‑109 (MQ=255)

                                                                                                   gTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GC‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGa                                                                                    <  2:1081419/86‑1 (MQ=255)

                                                                                                   gTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GC‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGa                                                                                    >  1:1081419/1‑86 (MQ=255)

                                                                                                       ccgccgATAGTGGTTTTAGCGACACGCAGT‑GC‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATAtt                                                            >  2:576790/1‑106 (MQ=255)

                                                                                                       ccgccgATAGTGGTTTTAGCGACACGCAGT‑GC‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATAtt                                                            <  1:576790/106‑1 (MQ=255)

                                                                                                       ccgccgATAGTGGTTTTAGCGACACGCAGT‑GC‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTc                           >  1:15030/1‑139 (MQ=255)

                                                                                                                           gACACGCAGT‑GC‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTccc       <  1:370010/139‑1 (MQ=255)

                                                                                                                             cacGCAGT‑GCCCCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCg                                                                          <  2:552863/71‑1 (MQ=255)

                                                                                                                             cacGCAGT‑GCCCCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCg                                                                          >  1:552863/1‑71 (MQ=255)

                                                                                                                             cacGCAGT‑GCCCCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTTTGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCAAAAGCAATTTcccc      >  1:692976/1‑139 (MQ=255)

                                                                                                                             cacGCAGT‑GC‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGc                                                                         >  2:34080/1‑71 (MQ=255)

                                                                                                                             cacGCAGT‑GC‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGc                                                                         <  1:34080/71‑1 (MQ=255)

                                                                                                                                gCAGT‑GC‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTCATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTcccccccc  <  2:1088682/139‑1 (MQ=255)

CATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑G‑‑CCCCCCC‑CAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCC  >  NC_000913/1593991‑1594256

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A