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
A3 F1 I2 R1	777	59.2	2955938	92.5%	2734242	106.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,961,562	C→T	H296Y (CAC→TAC)	rep →	DNA helicase and single‑stranded DNA‑dependent ATPase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,961,562	0	C	T	98.0%	155.6 / NA	50	H296Y (CAC→TAC)	rep	DNA helicase and single‑stranded DNA‑dependent ATPase
Reads supporting (aligned to +/- strand): ref base C (0/1); new base T (22/27); total (22/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCGCGGTGCACGTCCGCAAAACCTGGTGCTGCTGAGTCAGGATTTTCCGGCGCTGAAGGTGATTAAGCTTGAGCAGAACTATCGCTCTTCCGGGCGTATTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGCACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTATGGCGCGGAGCTAAAAGTATTAAGCGCGAATAACGAAGAACATGAGGCTGAGCGCGTTACTGGCGAGCTGATCGCCCATCACTTCGTCAATAAAACGC  >  NC_000913/3961426‑3961697

gcgcGGTGCACGTCCGCAAAACCTGGTGCTGCTGAGTCAGGATTTTCCGGCGCTGAAGGTGATTAAGCTTGAGCAGAACTATCGCTCTGCCGGGCGTATTCTCAAAGCGGCGAACATCCTGATCGCCAATAACCCGTAc                                                                                                                                       >  2:931637/1‑139 (MQ=255)

     gTGCACGTCCGCAAAACCTGGTGCTGCTGAGTCAGGATTTTCCGGCGCTGAAGGTGATTAAGCTTGAGCAGAACTATCGCTCTTCCGGGCGTATTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCtt                                                                                                                                  <  2:655030/139‑1 (MQ=255)

     gTGCACGTCCGCAAAACCTGGTGCTGCTGAGTCAGGATTTTCCGGCGCTGAAGGTGATTAAGCTTGAGCAGAACTATCGCTCTTCCGGGCGTATTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCtt                                                                                                                                  <  2:194701/139‑1 (MQ=255)

     gTGCACGTCCGCAAAACCTGGTGCTGCTGAGTCAGGATTTTCCGGCGCTGAAGGTGATTAAGCTTGAGCAGAACTATCGCTCTTCCGGGCGTATTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCtt                                                                                                                                  >  1:450911/1‑139 (MQ=255)

          cGTCCGCAAAACCTGGTGCTGCTGAGTCAGGATTTTCCGGCGCTGAAGGTGATTAAGCTTGAGCAGAACTATCGCTCTTCCGGGCGTATTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCTTTGaaa                                                                                                                             <  2:1056101/139‑1 (MQ=255)

          cGTCCGCAAAACCTGGTGCTGCTGAGTCAGGATTTTCCGGCGCTGAAGGTGATTAAGCTTGAGCAGAACTATCGCTCTTCCGGGCGTATTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCTTTGaaa                                                                                                                             <  1:278640/139‑1 (MQ=255)

               gCAAAACCTGGTGCTGCTGAGTCAGGATTTTCCGGCGCTGAAGGTGATTAAGCTTGAGCAGAACTATCGCTCTTCCGGGCGTATTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGt                                                                                                                        <  1:564261/139‑1 (MQ=255)

                cAAAACCTGGTGCTGCTGAGTCAGGATTTTCCGGCGCTGAAGGTGATTAAGCTTGAGCAGAACTATCGCTCTTCCGGGCGTATTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGTc                                                                                                                       >  1:860105/1‑139 (MQ=255)

                cAAAACCTGGTGCTGCTGAGTCAGGATTTTCCGGCGCTGAAGGTGATTAAGCTTGAGCAGAACTATCGCTCTTCCGGGCGTATTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGTc                                                                                                                       >  1:260080/1‑139 (MQ=255)

                cAAAACCTGGTGCTGCTGAGTCAGGATTTTCCGGCGCTGAAGGTGATTAAGCTTGAGCAGAACTATCGCTCTTCCGGGCGTATTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGTc                                                                                                                       >  1:629608/1‑139 (MQ=255)

                      cTGGTGCTGCTGAGTCAGGATTTTCCGGCGCTGAAGGTGATTAAGCTTGAGCAGAACTATCGCTCTTCCGGGCGTATTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGTCTGTtct                                                                                                                 <  1:1470581/139‑1 (MQ=255)

                                tgAGTCAGGATTTTCCGGCGCTGAAGGTGATTAAGCTTGAGCAGAACTATCGCTCTTCCGGGCGTATTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTggg                                                                                                       >  1:203862/1‑139 (MQ=255)

                                    tCAGGATTTTCCGGCGCTGAAGGTGATTAAGCTTGAGCAGAACTATCGCTCTTCCGGGCGTATTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTAt                                                                                                   >  1:1098326/1‑139 (MQ=255)

                                    tCAGGATTTTCCGGCGCTGAAGGTGATTAAGCTTGAGCAGAACTATCGCTCTTCCGGGCGTATTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTAt                                                                                                   >  1:740866/1‑139 (MQ=255)

                                         aTTTTCCGGCGCTGAAGGTGATTAAGCTTGAGCAGAACTATCGCTCTTCCGGGCGTATTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTATGgcgc                                                                                              <  2:260080/139‑1 (MQ=255)

                                         aTTTTCCGGCGCTGAAGGTGATTAAGCTTGAGCAGAACTATCGCTCTTCCGGGCGTATTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTATGgcgc                                                                                              <  1:1218400/139‑1 (MQ=255)

                                         aTTTTCCGGCGCTGAAGGTGATTAAGCTTGAGCAGAACTATCGCTCTTCCGGGCGTATTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTATGgcgc                                                                                              <  1:1216248/139‑1 (MQ=255)

                                          ttttCCGGCGCTGAAGGTGATTAAGCTTGAGCAGAACTATCGCTCTTCCGGGCGTATTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTATGGcgcg                                                                                             <  2:860105/139‑1 (MQ=255)

                                          ttttCCGGCGCTGAAGGTGATTAAGCTTGAGCAGAACTATCGCTCTTCCGGGCGTATTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTATGGcgcg                                                                                             <  2:1098326/139‑1 (MQ=255)

                                           tttCCGGCGCTGAAGGTGATTAAGCTTGAGCAGAACTATCGCTCTTCCGGGCGTATTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGCACGTCTTTGAAAAGCCTCTGTTCTCCGAACTGGGTTATGGCGCgg                                                                                            <  1:848598/139‑1 (MQ=255)

                                              ccGGCGCTGAAGGTGATTAAGCTTGAGCAGAACTATCGCTCTTCCGGGCGTATTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTATGGCGCgg                                                                                            <  2:937325/136‑1 (MQ=255)

                                              ccGGCGCTGAAGGTGATTAAGCTTGAGCAGAACTATCGCTCTTCCGGGCGTATTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTATGGCGCgg                                                                                            >  1:937325/1‑136 (MQ=255)

                                                  cgcTGAAGGTGATTAAGCTTGAGCAGAACTATCGCTCTTCCGGGCGTATTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTATGGCGCGGAGCTaaa                                                                                     <  2:1396876/139‑1 (MQ=255)

                                                                      gAGCAGAACTATCGCTCTTCCGGGCGTATTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTATGGCGCGGAGCTAAAAGTATTAAGCGCGAATAACg                                                                 <  2:1214122/139‑1 (MQ=255)

                                                                       aGCAGAACTATCGCTCTTCCGGGCGTATTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTATGgcgc                                                                                              <  1:752103/109‑1 (MQ=255)

                                                                       aGCAGAACTATCGCTCTTCCGGGCGTATTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTATGgcgc                                                                                              >  2:752103/1‑109 (MQ=255)

                                                                            aaCTATCGCTCTTCCGGGCGTATTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTATGGCGCGGAGCTAAAAGTATTAAGCGCGAATAACGAAGAAc                                                           >  2:27713/1‑139 (MQ=255)

                                                                             aCTATCGCTCTTCCGGGCGTATTCTG‑AAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTATGGCGCGGAGCTAAAAGTATTAAGCGCGAATAACGAAGAACAt                                                         >  2:569351/1‑139 (MQ=255)

                                                                                 tCGCTCTTCCGGGCGTATTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTATGGCGCGGAGCTAAAAGTATTAAGCGCGAATAACGAAGAACATGAg                                                      >  2:1268344/1‑139 (MQ=255)

                                                                                        tCCGGGCGTATTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTATGGCGCGGAGCTAAAAGTATTAAGCGCGAATaa                                                                   <  2:1307050/119‑1 (MQ=255)

                                                                                        tCCGGGCGTATTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTATGGCGCGGAGCTAAAAGTATTAAGCGCGAATaa                                                                   >  1:1307050/1‑119 (MQ=255)

                                                                                            ggCGTATTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTATGGCGCGGAGCTAAAAGTATTAAGCGCGAATAACGAAGAACATGAGGCTGAg                                                >  1:340514/1‑134 (MQ=255)

                                                                                            ggCGTATTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTATGGCGCGGAGCTAAAAGTATTAAGCGCGAATAACGAAGAACATGAGGCTGAg                                                <  2:340514/134‑1 (MQ=255)

                                                                                                 aTTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTATGGCGCGGAGCTAAAAGTATTAAGCGCGAATaa                                                                   <  2:844331/110‑1 (MQ=255)

                                                                                                 aTTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTATGGCGCGGAGCTAAAAGTATTAAGCGCGAATaa                                                                   >  1:844331/1‑110 (MQ=255)

                                                                                                    cTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTATGGCGCGGAGCTAAAAGTATTAAGCGCGAATAACGAAGAACATGAGGCTGAGCGCGTTACTGGCg                                   <  2:740866/139‑1 (MQ=255)

                                                                                                          gcggcgAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGt                                                                                                                        <  2:812792/48‑1 (MQ=255)

                                                                                                          gcggcgAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGt                                                                                                                        >  1:812792/1‑48 (MQ=255)

                                                                                                            ggcgAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGTCTGTtct                                                                                                                 >  1:901259/1‑53 (MQ=255)

                                                                                                            ggcgAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTATGGCGCGGAGCTAAAAGTATTAAGCGCGAATAACGAAGAACATGAGGCTGAGCGCGTTACTGGCGAGCTGATc                           >  1:1107432/1‑139 (MQ=255)

                                                                                                            gacgAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGTCTGTtct                                                                                                                 <  2:901259/51‑1 (MQ=255)

                                                                                                             gcgAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTATGGCGCgg                                                                                            <  2:802090/73‑1 (MQ=255)

                                                                                                             gcgAACATCCTGATCGCCAATAACCCGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTATGGCGCgg                                                                                            >  1:802090/1‑73 (MQ=255)

                                                                                                                        gATCGCCAATAACCCGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTATGGCGCGGAGCTAAAAGTATTAAGCGCGAATAACGAAGAACATGAGGCTGAGCGCGTTACTGGCGAGCTGATCGCCCATCACTTc               <  1:569351/139‑1 (MQ=255)

                                                                                                                             ccAATAACCCGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTATGGCGCGGAGCTAAAAGTATTAAGCGCGAATAACGAAGAACATGAGGCTGAGCGCGTTACTGGCGAGCTGATCGCCCATCACTTCGTCaa          >  2:217220/1‑139 (MQ=255)

                                                                                                                               aaTAACCCGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTATGGCGCGGAGCTAAAAGTATTAAGCGCGAATAACGAAGAACATGAGGCTGAGCGCGTTACTGGCGAGCTGATCGCCCATCACTTCGTCAATa        >  2:96395/1‑139 (MQ=255)

                                                                                                                                   aCCCGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTATGGCGCGGAGCTAAAAGTATTAAGCGCGAATAACGAAGAACATGAGGCTGAGCGCGTTACTGGCGAGCTGATCGCCCATCACTTCGTCAATAAAAc    <  1:217220/139‑1 (MQ=255)

                                                                                                                                    cccGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTATGGCGCGGAGCTAAAAGTATTAAGCGCGAATAACGAAGAACATGAGGCTGAGCGCGTTACTGGCGAGCTGATCGCCCATCACTTCGTCAATAAAACg   <  2:450911/139‑1 (MQ=255)

                                                                                                                                     ccGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTATGGCGCGGAGCTAAAAGTATTAAGCGCGAATAACGAAGAACATGAGGCTGAGCGCGTTACTGGCGAGCTGATCGCCCATCACTTCGTCAATAAAACGc  <  2:629608/139‑1 (MQ=255)

                                                                                                                                     ccGTACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTATGGCGCGGAGCTAAAAGTATTAAGCGCGAATAACGAAGAACATGAGGCTGAGCGCGTTACTGGCGAGCTGATCGCCCATCACTTCGTCAATAAAACGc  <  2:203862/139‑1 (MQ=255)

GCGCGGTGCACGTCCGCAAAACCTGGTGCTGCTGAGTCAGGATTTTCCGGCGCTGAAGGTGATTAAGCTTGAGCAGAACTATCGCTCTTCCGGGCGTATTCTGAAAGCGGCGAACATCCTGATCGCCAATAACCCGCACGTCTTTGAAAAGCGTCTGTTCTCCGAACTGGGTTATGGCGCGGAGCTAAAAGTATTAAGCGCGAATAACGAAGAACATGAGGCTGAGCGCGTTACTGGCGAGCTGATCGCCCATCACTTCGTCAATAAAACGC  >  NC_000913/3961426‑3961697

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