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
A19 F57 I0 R1 85 36.1 800162 93.0% 744150 140.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,343,438 C→T 36.0% intergenic (+114/+250) USA300HOU_2200 → / ← alsD hypothetical protein/acetolactate decarboxylase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,343,4380CT36.0% 27.4 / 20.9 33intergenic (+114/+250)USA300HOU_2200/alsDhypothetical protein/acetolactate decarboxylase
Reads supporting (aligned to +/- strand):  ref base C (8/13);  new base T (6/6);  total (14/19)
Fisher's exact test for biased strand distribution p-value = 7.16e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATACAAATTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTTATTTTATTACTTAGACG  >  CP000730/2343304‑2343569
                                                                                                                                      |                                                                                                                                   
aaacaaaataaaattAAATAATAATTTGAAAATAGTTTTATAAAAAAAAAAAAAAAAAATGGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGt                                                                                                                               <  2:65130/128‑1 (MQ=255)
 tACAAATTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTGGGAAATGATGGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTa                                                                                                                              >  2:382612/1‑141 (MQ=255)
   cAAATTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTaaa                                                                                                                            >  1:114252/1‑141 (MQ=255)
     aaTTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAAtt                                                                                                                          >  2:78953/1‑141 (MQ=255)
                     taatTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACTCGACGGAATTTTATATGAGTGTGTAc                                                                                                          <  1:293438/141‑1 (MQ=255)
                        tttGAAAATAGTTTTATAGGGCAAGCGCTGAAACATTGGCGTTTGTATTTTTAGTTACAGCAATTGTAAATTGATGCTGTTTTCTTGTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACcac                                                                                                       <  1:78953/141‑1 (MQ=255)
                              aagaGTTGTATAGGGCAAGCGCTTGAAAAGTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAACAGTAAATTTTATATGAGTGTGTACCACAATTta                                                                                                 <  2:173900/138‑1 (MQ=255)
                              aaTAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGATACACGGTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTta                                                                                                 <  1:171456/141‑1 (MQ=255)
                               aTAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATGGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTtat                                                                                                <  1:307919/141‑1 (MQ=255)
                                tAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTtata                                                                                               >  1:23375/1‑141 (MQ=255)
                                              aaccgcAGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCCTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACa                                                                                 <  2:246896/138‑1 (MQ=255)
                                               aGCGCTGAAAAATGGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTTTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTGATATGAGTGTGTACCACAATTTATAATCTAAACATAAcgg                                                                                <  2:29126/141‑3 (MQ=255)
                                                   cTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCaaa                                                                            >  1:337620/1‑141 (MQ=255)
                                                      aaaaaTTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAAtct                                                                         <  2:28742/141‑1 (MQ=255)
                                                          aTTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATCTATAATCTAAACATAACAGCAAATCTCaaa                                                                     <  1:111007/141‑1 (MQ=255)
                                                                         tttAGTTAGTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCtaat                                                      <  1:245545/141‑1 (MQ=255)
                                                                            ggTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATaaa                                                   <  1:196006/140‑1 (MQ=255)
                                                                                       ttGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCacta                                        <  2:23375/141‑1 (MQ=255)
                                                                                         gTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCactact                                      >  1:49581/1‑141 (MQ=255)
                                                                                            aaTTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAGATTTTAGATGAGTGTGTACCACAATTTATCATATAACCCGTACAGCAAATCTCAGATATCTGGAACCTAATGAATCCCCCCACTAATGCt                                   >  1:351321/1‑141 (MQ=255)
                                                                                            aaTTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCt                                   <  1:221984/141‑1 (MQ=255)
                                                                                                attGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATa                               <  1:44982/141‑1 (MQ=255)
                                                                                                      gttTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAg                         >  1:100400/1‑141 (MQ=255)
                                                                                                      gttTGCTTCTCGTAGTAACAGATTGGCCTATATAATAGTAAATTTTATATCCGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAg                         >  1:154910/1‑141 (MQ=255)
                                                                                                       tttGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTTCTAATAGTGAAgg                        <  1:99301/141‑1 (MQ=255)
                                                                                                                cGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCAGAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTAGTGCTAATAGTGAGGGGatttatat               >  2:171649/1‑139 (MQ=255)
                                                                                                                cGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATCTCTGGAACCTAATAAATCCCCTCACTACCGCTAATAGTGAAGGGatttattt               >  2:69118/1‑141 (MQ=255)
                                                                                                                  tagtaACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATATTGAAGGGAtttatttta             >  1:178527/1‑141 (MQ=255)
                                                                                                                   agtaACAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGAtttattttat            >  2:238070/1‑141 (MQ=255)
                                                                                                                     taACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTTATTttatta          <  2:312818/141‑1 (MQ=255)
                                                                                                                     taACAGAGTGGCCCATACCATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTTATTttatta          <  2:106028/141‑1 (MQ=255)
                                                                                                                       aCAGATTGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTTATTTTATTACt        >  2:305332/1‑141 (MQ=255)
                                                                                                                             tGGCCTATATAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAATCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTTATTGTATTACTTAGACg  <  2:348509/141‑1 (MQ=255)
                                                                                                                                      |                                                                                                                                   
ATACAAATTGTAGTTAAATAATAATTTGAAAATAGTTTTATAGGGCAAGCGCTGAAAAATTGGCGTTTGTCTTTTTAGTTATTGAACTTGTAAATTATTGTTGTTTGCTTCTCGTAGTAACAGATTGGCCTATACAATAGTAAATTTTATATGAGTGTGTACCACAATTTATAATCTAAACATAACAGCAAATCTCAAATATCTGGAACCTAATAAATCCCCTCACTACTGCTAATAGTGAAGGGATTTATTTTATTACTTAGACG  >  CP000730/2343304‑2343569

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A