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 F17 I1 R1 20 35.2 1573650 87.5% 1376943 142.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,196,232 C→T T370T (ACC→ACT)  icd → isocitrate dehydrogenase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,196,2320CT94.1% 42.5 / ‑6.4 17T370T (ACC→ACT) icdisocitrate dehydrogenase
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base T (7/9);  total (7/10)
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

CAAACATCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTT  >  NC_000913/1196099‑1196300
                                                                                                                                     |                                                                    
cAAACATCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCt                                                             >  1:520469/1‑143 (MQ=255)
   aCATCGGTGACGAATGCGCCCTGTTTGAAGCCAACAACGGTACTGCGACGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCAGAGATGATGCTGCACCATATAGGTAAGACTGAAACGGcatac                                                          >  2:485090/1‑139 (MQ=255)
               aaTGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTaaa                                              <  2:199612/143‑1 (MQ=38)
               aaTGCGCCCGGGTTGAGGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTaaa                                              <  2:502805/143‑1 (MQ=37)
                aggcgcCCTGTTTGAAGCCCCCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAg                                             <  1:78400/141‑1 (MQ=37)
                aTGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAg                                             <  1:734219/143‑1 (MQ=38)
                      ccTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGACACGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATgg                                       >  1:359947/1‑143 (MQ=37)
                       cTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGGAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGAGTGTTAAAGGTATGGa                                      >  1:403150/1‑143 (MQ=37)
                          tttGAAGCAACCCTCGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAgg                                   <  2:667088/143‑1 (MQ=25)
                           ttGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGgc                                  <  1:501489/143‑1 (MQ=255)
                             caaGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAAGCCTGTCTGTATTATTCTCTGCGCTGTGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGgcgc                                <  2:251370/142‑1 (MQ=21)
                               aGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGCTAAAGGAATGGGAGTCGCaa                              >  2:301670/1‑143 (MQ=37)
                                    cccacGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCaat                         <  1:575113/143‑2 (MQ=25)
                                     ccacGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCAATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACATGATTGTTAAAGGTATGGAAAGCGCAAACaatg                        >  2:245217/1‑141 (MQ=25)
                                         ggTACTGCTCCGAGAGACGCCCGTCAGGACAAAGTAAATCCTGGCTCTATTATGCTCTCCGCTGAGATGCTGCTGCGCCATATGGGTTGGACCGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCaa                    <  2:541264/143‑1 (MQ=18)
                                                           gCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACtt  <  2:357367/143‑1 (MQ=17)
                                                           gCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCCGCTGACCTGATTGTCAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGAcct  >  1:605992/1‑141 (MQ=17)
                                                                                                                                     |                                                                    
CAAACATCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTT  >  NC_000913/1196099‑1196300

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A